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FAM20A FAM20A golgi associated secretory pathway pseudokinase [ Homo sapiens (human) ]

Gene ID: 54757, updated on 3-Apr-2024

Summary

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Official Symbol
FAM20Aprovided by HGNC
Official Full Name
FAM20A golgi associated secretory pathway pseudokinaseprovided by HGNC
Primary source
HGNC:HGNC:23015
See related
Ensembl:ENSG00000108950 MIM:611062; AllianceGenome:HGNC:23015
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
AI1G; AIGFS; FP2747
Summary
This locus encodes a protein that is likely secreted and may function in hematopoiesis. A mutation at this locus has been associated with amelogenesis imperfecta and gingival hyperplasia syndrome. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Aug 2011]
Expression
Broad expression in salivary gland (RPKM 7.2), liver (RPKM 6.1) and 23 other tissues See more
Orthologs
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Genomic context

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See FAM20A in Genome Data Viewer
Location:
17q24.2
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (68535116..68601367, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (69411970..69478232, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (66531257..66597508, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene arylsulfatase G Neighboring gene tRNA-undetermined (NNN) 5-1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66409262-66409920 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66409921-66410577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:66432181-66432681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8900 Neighboring gene protein kinase cAMP-dependent type I regulatory subunit alpha Neighboring gene ReSE screen-validated silencer GRCh37_chr17:66453793-66454079 Neighboring gene microRNA 635 Neighboring gene WD repeat domain, phosphoinositide interacting 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8902 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:66494688-66494871 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:66508045-66508618 Neighboring gene Sharpr-MPRA regulatory region 15560 Neighboring gene Sharpr-MPRA regulatory region 13674 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:66627729-66628228 Neighboring gene long intergenic non-protein coding RNA 1482 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:66682485-66682986 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:66682987-66683486 Neighboring gene uncharacterized LOC124904049

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. FAM20A mutations and transcriptome analyses of dental pulp tissues of enamel renal syndrome. Wang SK, et al. Int Endod J, 2023 Aug. PMID 37159186,
  2. Two new families with enamel renal syndrome: A novel FAM20A gene mutation and review of literature. Hassib NF, et al. Eur J Med Genet, 2020 Nov. PMID 32835847
  3. Four novel mutations of FAM20A in amelogenesis imperfecta type IG and review of literature for its genotype and phenotype spectra. Nitayavardhana I, et al. Mol Genet Genomics, 2020 Jul. PMID 32246227
  4. Enamel renal syndrome: A novel homozygous FAM20A founder mutation in 5 new Brazilian families. Dourado MR, et al. Eur J Med Genet, 2019 Nov. PMID 30394349
  5. Physicochemical analysis of human pulpal mineralization secondary to FAM20A mutations. Berès F, et al. Connect Tissue Res, 2018 Dec. PMID 29745815

See all (26) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. FAM20A-Associated Amelogenesis Imperfecta: Gene Variants with Functional Verification and Histological Features.
    Title: FAM20A-Associated Amelogenesis Imperfecta: Gene Variants with Functional Verification and Histological Features.
  2. FAM20A is a golgi-localized Type II transmembrane protein.
    Title: FAM20A is a golgi-localized Type II transmembrane protein.
  3. Deep dental phenotyping and a novel FAM20A variant in patients with amelogenesis imperfecta type IG.
    Title: Deep dental phenotyping and a novel FAM20A variant in patients with amelogenesis imperfecta type IG.
  4. FAM20A mutations and transcriptome analyses of dental pulp tissues of enamel renal syndrome.
    Title: FAM20A mutations and transcriptome analyses of dental pulp tissues of enamel renal syndrome.
  5. Two new families with enamel renal syndrome: A novel FAM20A gene mutation and review of literature.
    Title: Two new families with enamel renal syndrome: A novel FAM20A gene mutation and review of literature.
  6. Whole exome sequencing (WES) identified that Pt-1 was heterozygous for FAM20A, c.758A > G (p.Tyr253Cys), inherited from her father. The mutation on maternal allele was not detected by WES. Pt-2 possessed compound heterozygous mutations, c.1248dupG (p.Phe417Valfs*7); c.1081C > T (p.Arg361Cys) in FAM20A.
    Title: Four novel mutations of FAM20A in amelogenesis imperfecta type IG and review of literature for its genotype and phenotype spectra.
  7. Here we report the largest series of patients with Enamel renal syndrome in a same population, and describe, for the first time, a founder mutation for FAM20A.
    Title: Enamel renal syndrome: A novel homozygous FAM20A founder mutation in 5 new Brazilian families.
  8. Mutations in LAMB3 and FAM20A were found in 3 Turkish families with Amelogenesis imperfecta
    Title: Candidate gene sequencing reveals mutations causing hypoplastic amelogenesis imperfecta.
  9. Recessive FAM20A mutations can cause nephrocalcinosis in addition to the oral phenotype
    Title: Nephrocalcinosis in Amelogenesis Imperfecta Caused by the FAM20A Mutation.
  10. Physicochemical analysis of human pulpal mineralization secondary to FAM20A mutations.
    Title: Physicochemical analysis of human pulpal mineralization secondary to FAM20A mutations.
Submit: New GeneRIF Correction See all GeneRIFs (21)

Phenotypes

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

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Amelogenesis imperfecta type 1G
MedGen: C2931783 OMIM: 204690 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp434F2322

Gene Ontology Provided by GOA

Function Evidence Code Pubs
NOT enables phosphotransferase activity, alcohol group as acceptor IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein serine/threonine kinase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein serine/threonine kinase activator activity IDA
Inferred from Direct Assay
more info
 PubMed 
NOT enables protein serine/threonine kinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in biomineral tissue development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in calcium ion homeostasis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in enamel mineralization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in enamel mineralization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of protein phosphorylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of protein phosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
  
NOT involved_in protein phosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in response to bacterium IEA
Inferred from Electronic Annotation
more info
  
involved_in tooth eruption IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
colocalizes_with Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
  
colocalizes_with Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in endoplasmic reticulum ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in extracellular exosome HDA PubMed 
located_in extracellular space IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
pseudokinase FAM20A
Names
family with sequence similarity 20, member A
protein FAM20A

NCBI Reference Sequences (RefSeq)

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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.

Genomic

  1. NG_029809.1 RefSeqGene

    Range
    4588..70839
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001243746.2 → NP_001230675.1  pseudokinase FAM20A isoform b

    See identical proteins and their annotated locations for NP_001230675.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate exon at its 5' end and uses a downstream start codon, compared to variant 1. The encoded protein (isoform b) has a shorter N-terminus compared to isoform a.
    Source sequence(s)
    AC079210, AK298071, AL133105, AY358197, BC036222
    UniProtKB/TrEMBL
    B7Z4Y3
    Conserved Domains (1) summary
    cd10469
    Location:168 → 384
    FAM20A_C; C-terminal putative kinase domain of FAM20A

  2. NM_017565.4 → NP_060035.2  pseudokinase FAM20A isoform a precursor

    See identical proteins and their annotated locations for NP_060035.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a).
    Source sequence(s)
    AC079210, AL133105, AY358197, BC036222, BC136686, CB530015, N64017
    Consensus CDS
    CCDS11679.1
    UniProtKB/Swiss-Prot
    B2RN47, B2RN49, Q96MK3, Q9UF95
    UniProtKB/TrEMBL
    L8B8N7
    Related
    ENSP00000468308.1, ENST00000592554.2
    Conserved Domains (1) summary
    cd10469
    Location:306 → 522
    FAM20A_C; C-terminal putative kinase domain of FAM20A

RNA

  1. NR_027751.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has multiple differences compared to variant 1. The transcript is sufficiently abundant to represent as a RefSeq record; however, the predicted protein is not represented because there is uncertainty about the protein-coding capacity of the transcript.
    Source sequence(s)
    AC079210, AL133105, BC036222, CB530015, DB057818, N64017
    Related
    ENST00000226094.9

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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    68535116..68601367 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006721959.4 → XP_006722022.1  pseudokinase FAM20A isoform X1

    See identical proteins and their annotated locations for XP_006722022.1

    UniProtKB/TrEMBL
    B7Z4Y3
    Conserved Domains (1) summary
    cd10469
    Location:168 → 384
    FAM20A_C; C-terminal putative kinase domain of FAM20A

  2. XM_047436319.1 → XP_047292275.1  pseudokinase FAM20A isoform X3

  3. XM_017024781.3 → XP_016880270.1  pseudokinase FAM20A isoform X2

    Conserved Domains (1) summary
    cl05973
    Location:306 → 373
    FAM20_C_like; C-terminal putative kinase domain of FAM20 (family with sequence similarity 20), Drosophila Four-jointed (Fj), and related proteins

  4. XM_011524918.4 → XP_011523220.1  pseudokinase FAM20A isoform X4

    Conserved Domains (1) summary
    cl05973
    Location:306 → 370
    FAM20_C_like; C-terminal putative kinase domain of FAM20 (family with sequence similarity 20), Drosophila Four-jointed (Fj), and related proteins

RNA

  1. XR_002958041.2 RNA Sequence

  2. XR_934487.4 RNA Sequence

  3. XR_001752543.3 RNA Sequence

  4. XR_429905.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    69411970..69478232 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054316546.1 → XP_054172521.1  pseudokinase FAM20A isoform X1

  2. XM_054316548.1 → XP_054172523.1  pseudokinase FAM20A isoform X3

  3. XM_054316547.1 → XP_054172522.1  pseudokinase FAM20A isoform X2

  4. XM_054316549.1 → XP_054172524.1  pseudokinase FAM20A isoform X4

RNA

  1. XR_008484843.1 RNA Sequence

  2. XR_008484844.1 RNA Sequence

  3. XR_008484845.1 RNA Sequence

  4. XR_008484846.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96MK3.4 GenPept UniProtKB/Swiss-Prot:Q96MK3

Gene LinkOut

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