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SMIM1 small integral membrane protein 1 (Vel blood group) [ Homo sapiens (human) ]

Gene ID: 388588, updated on 7-Apr-2024

Summary

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Official Symbol
SMIM1provided by HGNC
Official Full Name
small integral membrane protein 1 (Vel blood group)provided by HGNC
Primary source
HGNC:HGNC:44204
See related
Ensembl:ENSG00000235169 MIM:615242; AllianceGenome:HGNC:44204
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
Vel
Summary
This gene encodes a small, conserved protein that participates in red blood cell formation. The encoded protein is localized to the cell membrane and is the antigen for the Vel blood group. Alternative splicing results in different transcript variants that encode the same protein. [provided by RefSeq, Dec 2013]
Expression
Broad expression in testis (RPKM 6.7), bone marrow (RPKM 6.0) and 14 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
1p36.32
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (3772749..3775956)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (3284345..3287549)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (3689313..3692520)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene tumor protein p73 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3661686-3662521 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3662522-3663358 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 123 Neighboring gene Gfo/Idh/MocA-like oxidoreductase domain containing 3, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3678785-3679286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3679287-3679786 Neighboring gene coiled-coil domain containing 27 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3687696-3688374 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3689661-3690176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3690177-3690692 Neighboring gene MPRA functional variant 1:3691528:A:G red blood cell enhancer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3691725-3692240 Neighboring gene RNA, 7SL, cytoplasmic 574, pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:3709930-3710608 Neighboring gene leucine rich repeat containing 47 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 125 Neighboring gene Sharpr-MPRA regulatory region 1968 Neighboring gene centrosomal protein 104 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:3745882-3747081 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:3747165-3748364 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:3755401-3755900 Neighboring gene uncharacterized LOC124903829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3767162-3767662

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. SMIM1 missense mutations exert their effect on wild type Vel expression late in erythroid differentiation. van der Rijst MVE, et al. Transfusion, 2021 Jan. PMID 33128268
  2. SMIM1, carrier of the Vel blood group, is a tail-anchored transmembrane protein and readily forms homodimers in a cell-free system. Nylander A, et al. Biosci Rep, 2020 May 29. PMID 32301496, Free PMC Article
  3. Dimerization of small integral membrane protein 1 promotes cell surface presentation of the Vel blood group epitope. Kelley LP, et al. FEBS Lett, 2020 Apr. PMID 31879955
  4. Identification of a novel single-nucleotide mutation in SMIM1 gene that results in low Vel antigen expression. van der Rijst MVE, et al. Transfusion, 2019 Oct. PMID 31218697, Free PMC Article
  5. SMIM1 polymorphisms in a donor population from southeast Brazil and their correlation with VEL expression. Arnoni CP, et al. Blood Transfus, 2019 Jan. PMID 29517970, Free PMC Article

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SMIM1 missense mutations exert their effect on wild type Vel expression late in erythroid differentiation.
    Title: SMIM1 missense mutations exert their effect on wild type Vel expression late in erythroid differentiation.
  2. Dimerization of small integral membrane protein 1 promotes cell surface presentation of the Vel blood group epitope.
    Title: Dimerization of small integral membrane protein 1 promotes cell surface presentation of the Vel blood group epitope.
  3. SMIM1, carrier of the Vel blood group, is a tail-anchored transmembrane protein and readily forms homodimers in a cell-free system.
    Title: SMIM1, carrier of the Vel blood group, is a tail-anchored transmembrane protein and readily forms homodimers in a cell-free system.
  4. Identification of a novel single-nucleotide mutation in SMIM1 gene that results in low Vel antigen expression.
    Title: Identification of a novel single-nucleotide mutation in SMIM1 gene that results in low Vel antigen expression.
  5. the present study demonstrated that although the SMIM1*64_80del allele is responsible for some variation of Vel phenotype in this donor population, Vel expression is also controlled by molecular changes in SMIM1 intron 2.
    Title: SMIM1 polymorphisms in a donor population from southeast Brazil and their correlation with VEL expression.
  6. rs1175550G and to a lesser extent rs143702418C independently increase SMIM1 and Vel antigen expression.
    Title: SMIM1 variants rs1175550 and rs143702418 independently modulate Vel blood group antigen expression.
  7. Among the 448 samples analysed, 10 (2.23%) harboured the 17 bp deletion of the gene SMIM1, and all were heterozygote for the SMIM1*64_80 del allele.
    Title: Screening for the SMIM1*64_80 del Allele in blood donors in a population from Southern Brazil.
  8. Alleles that initially entered the population have been maintained within the population. The c.64_80del null allele of SMIM1 is one such allele, thus having implications for transfusion medicine and child or maternal health.
    Title: The c.64_80del SMIM1 allele is segregating in the Hutterite population.
  9. SMIM1 carries the Vel antigen as a type II membrane protein with a predicted C-terminal extracellular domain of only 3-12 amino acids
    Title: SMIM1 is a type II transmembrane phosphoprotein and displays the Vel blood group antigen at its carboxyl-terminus.
  10. Weak Vel expression levels are caused by multiple genetic factors in SMIM1 and probably also by other genetic or environmental factors.
    Title: Impact of genetic variation in the SMIM1 gene on Vel expression levels.
Submit: New GeneRIF Correction See all GeneRIFs (13)

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
Vel blood group system
MedGen: C2745907 OMIM: 615264 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Genome-wide association study identifies loci affecting blood copper, selenium and zinc.
EBI GWAS Catalog

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in cell surface IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cell surface IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 

General protein information

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Preferred Names
small integral membrane protein 1
Names
bloodgroup VEL protein
vel blood group antigen

NCBI Reference Sequences (RefSeq)

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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.

Genomic

  1. NG_033869.1 RefSeqGene

    Range
    4989..8196
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_827

mRNA and Protein(s)

  1. NM_001163724.3 → NP_001157196.1  small integral membrane protein 1

    See identical proteins and their annotated locations for NP_001157196.1

    Status: REVIEWED

    Source sequence(s)
    AL365330
    Consensus CDS
    CCDS57966.1
    UniProtKB/Swiss-Prot
    B2RUZ4
    UniProtKB/TrEMBL
    A0A5Q0LQ04, M4WDD3
    Related
    ENSP00000457386.1, ENST00000444870.7
    Conserved Domains (1) summary
    pfam15875
    Location:3 → 77
    DUF4731; Domain of unknown function (DUF4731)

  2. NM_001288583.2 → NP_001275512.1  small integral membrane protein 1

    See identical proteins and their annotated locations for NP_001275512.1

    Status: REVIEWED

    Source sequence(s)
    AL365330
    Consensus CDS
    CCDS57966.1
    UniProtKB/Swiss-Prot
    B2RUZ4
    UniProtKB/TrEMBL
    A0A5Q0LQ04, M4WDD3
    Related
    ENSP00000496314.2, ENST00000642557.4
    Conserved Domains (1) summary
    pfam15875
    Location:3 → 77
    DUF4731; Domain of unknown function (DUF4731)

  3. NM_001379690.1 → NP_001366619.1  small integral membrane protein 1

    Status: REVIEWED

    Source sequence(s)
    AL365330
    Consensus CDS
    CCDS57966.1
    UniProtKB/Swiss-Prot
    B2RUZ4
    UniProtKB/TrEMBL
    A0A5Q0LQ04, M4WDD3
    Conserved Domains (1) summary
    pfam15875
    Location:3 → 77
    DUF4731; Domain of unknown function (DUF4731)

  4. NM_001379691.1 → NP_001366620.1  small integral membrane protein 1

    Status: REVIEWED

    Source sequence(s)
    AL365330
    Consensus CDS
    CCDS57966.1
    UniProtKB/Swiss-Prot
    B2RUZ4
    UniProtKB/TrEMBL
    A0A5Q0LQ04, M4WDD3
    Conserved Domains (1) summary
    pfam15875
    Location:3 → 77
    DUF4731; Domain of unknown function (DUF4731)

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    3772749..3775956
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047420003.1 → XP_047275959.1  small integral membrane protein 1 isoform X1

    UniProtKB/Swiss-Prot
    B2RUZ4
    UniProtKB/TrEMBL
    M4WDD3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    3284345..3287549
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
B2RUZ4.1 GenPept UniProtKB/Swiss-Prot:B2RUZ4

Gene LinkOut

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