U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

CARMIL1 capping protein regulator and myosin 1 linker 1 [ Homo sapiens (human) ]

Gene ID: 55604, updated on 7-Apr-2024

Summary

Go to the top of the page Help
Official Symbol
CARMIL1provided by HGNC
Official Full Name
capping protein regulator and myosin 1 linker 1provided by HGNC
Primary source
HGNC:HGNC:21581
See related
Ensembl:ENSG00000079691 MIM:609593; AllianceGenome:HGNC:21581
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CARMIL; LRRC16; LRRC16A; CARMIL1a; dJ501N12.1; dJ501N12.5
Summary
Involved in several processes, including actin filament network formation; plasma membrane bounded cell projection organization; and positive regulation of cellular component organization. Located in several cellular components, including lamellipodium; macropinosome; and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 7.4), small intestine (RPKM 6.3) and 24 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See CARMIL1 in Genome Data Viewer
Location:
6p22.2
Exon count:
41
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (25279374..25620530)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (25145130..25486328)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (25279602..25620758)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928663 Neighboring gene katanin regulatory subunit B1 like 1 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16995 Neighboring gene ribosomal protein L21 pseudogene 68 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:25292659-25293159 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:25311331-25311831 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:25315887-25316577 Neighboring gene uncharacterized LOC124901281 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:25342051-25342783 Neighboring gene RNA, U6 small nuclear 987, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24169 Neighboring gene uncharacterized LOC124901546 Neighboring gene NANOG hESC enhancer GRCh37_chr6:25462672-25463208 Neighboring gene MPRA-validated peak5738 silencer Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:25504114-25505313 Neighboring gene MPRA-validated peak5739 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:25627151-25627701 Neighboring gene NANOG hESC enhancer GRCh37_chr6:25635867-25636368 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:25660432-25661631 Neighboring gene uncharacterized LOC124901284 Neighboring gene PRELID1 pseudogene 2 Neighboring gene secretagogin, EF-hand calcium binding protein

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Novel CARMIL2 Mutations in Patients with Variable Clinical Dermatitis, Infections, and Combined Immunodeficiency. Alazami AM, et al. Front Immunol, 2018. PMID 29479355, Free PMC Article
  2. A Missense Genetic Variant in LRRC16A/CARMIL1 Improves Acute Respiratory Distress Syndrome Survival by Attenuating Platelet Count Decline. Wei Y, et al. Am J Respir Crit Care Med, 2017 May 15. PMID 27768389, Free PMC Article
  3. Physiological role of the interaction between CARMIL1 and capping protein. Edwards M, et al. Mol Biol Cell, 2013 Oct. PMID 23904264, Free PMC Article
  4. Mechanism for CARMIL protein inhibition of heterodimeric actin-capping protein. Kim T, et al. J Biol Chem, 2012 May 4. PMID 22411988, Free PMC Article
  5. Allosteric Coupling of CARMIL and V-1 Binding to Capping Protein Revealed by Hydrogen-Deuterium Exchange. Johnson B, et al. Cell Rep, 2018 May 29. PMID 29847807, Free PMC Article

See all (58) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The Leucine-Rich Repeat Region of CARMIL1 Regulates IL-1-Mediated ERK Activation, MMP Expression, and Collagen Degradation.
    Title: The Leucine-Rich Repeat Region of CARMIL1 Regulates IL-1-Mediated ERK Activation, MMP Expression, and Collagen Degradation.
  2. V-1 and CARMIL induce changes in both proteins' binding sites on the surface of capping proteins, along with a set of internal residues.
    Title: Allosteric Coupling of CARMIL and V-1 Binding to Capping Protein Revealed by Hydrogen-Deuterium Exchange.
  3. Study utilized whole exome sequencing and other assays to genetically and functionally characterize three consanguineous multiplex Saudi families with CARMIL2 mutations, presenting with dermatitis, recurrent skin abscesses and chest infections.
    Title: Novel CARMIL2 Mutations in Patients with Variable Clinical Dermatitis, Infections, and Combined Immunodeficiency.
  4. A novel genetic variant in leucine-rich repeat-containing 16A (LRRC16A) has been associated with reduced ARDS risk.
    Title: A Missense Genetic Variant in LRRC16A/CARMIL1 Improves Acute Respiratory Distress Syndrome Survival by Attenuating Platelet Count Decline.
  5. LRRC16A plays a role in adult respiratory distress syndrome pathophysiology by interacting with, and being mediated through, platelets.
    Title: Platelet count mediates the contribution of a genetic variant in LRRC16A to ARDS risk.
  6. shown for the first time that CARMIL/LRRC16A was associated with gout, which could be due to urate transportsome failure
    Title: Common variant of leucine-rich repeat-containing 16A (LRRC16A) gene is associated with gout susceptibility.
  7. The results also suggest that the ability of CARMIL1 to inhibit CP in cells may be regulated.
    Title: Physiological role of the interaction between CARMIL1 and capping protein.
  8. Data suggest that CARMIL promotes uncapping by binding to a freely accessible site on Capping protein (CP) bound to a filament barbed end and inducing a change in the conformation of the actin-binding surface of CP.
    Title: Mechanism for CARMIL protein inhibition of heterodimeric actin-capping protein.
  9. The two CARMIL isoforms are both important for cell migration, but they have distinct functions.[CARMIL1, CARMIL2]
    Title: Distinct roles for CARMIL isoforms in cell migration.
  10. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction See all GeneRIFs (13)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A meta-analysis and genome-wide association study of platelet count and mean platelet volume in african americans.
EBI GWAS Catalog
Meta-analysis of 28,141 individuals identifies common variants within five new loci that influence uric acid concentrations.
EBI GWAS Catalog
New gene functions in megakaryopoiesis and platelet formation.
EBI GWAS Catalog
Variants in TF and HFE explain approximately 40% of genetic variation in serum-transferrin levels.
EBI GWAS Catalog

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

Go to the top of the page Help

Replication interactions

Interaction Pubs
Knockdown of leucine rich repeat containing 16A (LRRC16A) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • FLJ20048, FLJ43708

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-containing complex binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in actin filament network formation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in actin filament organization NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in barbed-end actin filament uncapping ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cell migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell migration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in lamellipodium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in macropinocytosis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of barbed-end actin filament capping ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of actin filament polymerization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of cell migration IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of cell migration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of lamellipodium organization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of stress fiber assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of substrate adhesion-dependent cell spreading IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of Arp2/3 complex-mediated actin nucleation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ruffle organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in urate metabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cell leading edge IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 
part_of filamentous actin ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in lamellipodium IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in lamellipodium IDA
Inferred from Direct Assay
more info
 PubMed 
located_in macropinosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

Go to the top of the page Help
Preferred Names
F-actin-uncapping protein LRRC16A
Names
CARMIL homolog
capping protein regulator and myosin 1 linker protein 1
capping protein, Arp2/3 and myosin-I linker homolog 1
capping protein, Arp2/3 and myosin-I linker protein 1
capping protein, Arp2/3, and Myosin-I Linker homolog 1
leucine rich repeat containing 16
leucine rich repeat containing 16A
leucine-rich repeat-containing protein 16A
testicular tissue protein Li 107

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001173977.2 → NP_001167448.1  F-actin-uncapping protein LRRC16A isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (2) lacks an internal 6-aa segment near the C-terminus, compared to isoform 1.
    Source sequence(s)
    AL022170, AL024509, AL160037
    Consensus CDS
    CCDS93871.1
    UniProtKB/TrEMBL
    A0A8V8TRE2, B2RTQ5
    Related
    ENSP00000515137.1, ENST00000700669.1
    Conserved Domains (4) summary
    cd00116
    Location:229 → 373
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:484 → 507
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:248 → 277
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam16000
    Location:786 → 1078
    CARMIL_C; CARMIL C-terminus

  2. NM_017640.6 → NP_060110.4  F-actin-uncapping protein LRRC16A isoform 1

    See identical proteins and their annotated locations for NP_060110.4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AL022170, AL024509, AL160037
    Consensus CDS
    CCDS54973.1
    UniProtKB/Swiss-Prot
    B8X1J0, Q5VZK9, Q6ZUH5, Q6ZW07, Q9NXU7
    UniProtKB/TrEMBL
    B2RTQ5
    Related
    ENSP00000331983.6, ENST00000329474.7
    Conserved Domains (4) summary
    cd00116
    Location:229 → 373
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:484 → 507
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:248 → 277
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam16000
    Location:786 → 1078
    CARMIL_C; CARMIL C-terminus

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    25279374..25620530
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017011008.2 → XP_016866497.1  F-actin-uncapping protein LRRC16A isoform X1

    UniProtKB/TrEMBL
    B2RTQ5

  2. XM_017011009.2 → XP_016866498.1  F-actin-uncapping protein LRRC16A isoform X2

    UniProtKB/TrEMBL
    B2RTQ5

  3. XM_017011015.2 → XP_016866504.1  F-actin-uncapping protein LRRC16A isoform X12

    UniProtKB/TrEMBL
    B2RTQ5

  4. XM_017011012.2 → XP_016866501.1  F-actin-uncapping protein LRRC16A isoform X5

    UniProtKB/TrEMBL
    B2RTQ5

  5. XM_024446484.2 → XP_024302252.1  F-actin-uncapping protein LRRC16A isoform X6

    UniProtKB/TrEMBL
    B2RTQ5
    Conserved Domains (5) summary
    sd00033
    Location:488 → 511
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:248 → 277
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam16000
    Location:790 → 1088
    CARMIL_C; CARMIL C-terminus
    cl26161
    Location:229 → 373
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    cl28033
    Location:1099 → 1348
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region

  6. XM_024446485.2 → XP_024302253.1  F-actin-uncapping protein LRRC16A isoform X14

    UniProtKB/TrEMBL
    B2RTQ5
    Conserved Domains (5) summary
    sd00033
    Location:488 → 511
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:248 → 277
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam16000
    Location:790 → 1088
    CARMIL_C; CARMIL C-terminus
    cl26161
    Location:229 → 373
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    cl28033
    Location:1099 → 1345
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region

  7. XM_017011011.2 → XP_016866500.1  F-actin-uncapping protein LRRC16A isoform X4

    UniProtKB/TrEMBL
    B2RTQ5

  8. XM_017011016.2 → XP_016866505.1  F-actin-uncapping protein LRRC16A isoform X13

    UniProtKB/TrEMBL
    B2RTQ5

  9. XM_017011013.2 → XP_016866502.1  F-actin-uncapping protein LRRC16A isoform X9

    UniProtKB/TrEMBL
    B2RTQ5

  10. XM_047418997.1 → XP_047274953.1  F-actin-uncapping protein LRRC16A isoform X15

  11. XM_017011010.2 → XP_016866499.1  F-actin-uncapping protein LRRC16A isoform X3

    UniProtKB/TrEMBL
    B2RTQ5

  12. XM_005249218.2 → XP_005249275.1  F-actin-uncapping protein LRRC16A isoform X7

    UniProtKB/TrEMBL
    B2RTQ5
    Conserved Domains (4) summary
    cd00116
    Location:229 → 373
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:484 → 507
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:248 → 277
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam16000
    Location:786 → 1078
    CARMIL_C; CARMIL C-terminus

  13. XM_047418994.1 → XP_047274950.1  F-actin-uncapping protein LRRC16A isoform X8

  14. XM_047418995.1 → XP_047274951.1  F-actin-uncapping protein LRRC16A isoform X10

  15. XM_047418996.1 → XP_047274952.1  F-actin-uncapping protein LRRC16A isoform X11

  16. XM_047418998.1 → XP_047274954.1  F-actin-uncapping protein LRRC16A isoform X16

  17. XM_047418999.1 → XP_047274955.1  F-actin-uncapping protein LRRC16A isoform X17

  18. XM_017011017.2 → XP_016866506.1  F-actin-uncapping protein LRRC16A isoform X18

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    25145130..25486328
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054355815.1 → XP_054211790.1  F-actin-uncapping protein LRRC16A isoform X1

  2. XM_054355816.1 → XP_054211791.1  F-actin-uncapping protein LRRC16A isoform X2

  3. XM_054355828.1 → XP_054211803.1  F-actin-uncapping protein LRRC16A isoform X12

  4. XM_054355819.1 → XP_054211794.1  F-actin-uncapping protein LRRC16A isoform X5

  5. XM_054355820.1 → XP_054211795.1  F-actin-uncapping protein LRRC16A isoform X6

  6. XM_054355830.1 → XP_054211805.1  F-actin-uncapping protein LRRC16A isoform X14

  7. XM_054355818.1 → XP_054211793.1  F-actin-uncapping protein LRRC16A isoform X4

  8. XM_054355829.1 → XP_054211804.1  F-actin-uncapping protein LRRC16A isoform X13

  9. XM_054355823.1 → XP_054211798.1  F-actin-uncapping protein LRRC16A isoform X9

  10. XM_054355831.1 → XP_054211806.1  F-actin-uncapping protein LRRC16A isoform X15

  11. XM_054355817.1 → XP_054211792.1  F-actin-uncapping protein LRRC16A isoform X3

  12. XM_054355821.1 → XP_054211796.1  F-actin-uncapping protein LRRC16A isoform X7

  13. XM_054355822.1 → XP_054211797.1  F-actin-uncapping protein LRRC16A isoform X8

  14. XM_054355824.1 → XP_054211799.1  F-actin-uncapping protein LRRC16A isoform X10

  15. XM_054355825.1 → XP_054211800.1  F-actin-uncapping protein LRRC16A isoform X19

  16. XM_054355826.1 → XP_054211801.1  F-actin-uncapping protein LRRC16A isoform X20

  17. XM_054355827.1 → XP_054211802.1  F-actin-uncapping protein LRRC16A isoform X11

  18. XM_054355832.1 → XP_054211807.1  F-actin-uncapping protein LRRC16A isoform X16

  19. XM_054355833.1 → XP_054211808.1  F-actin-uncapping protein LRRC16A isoform X17

  20. XM_054355834.1 → XP_054211809.1  F-actin-uncapping protein LRRC16A isoform X18

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5VZK9.1 GenPept UniProtKB/Swiss-Prot:Q5VZK9

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous