SLC45A2 solute carrier family 45 member 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC45A2provided by HGNC
Official Full Name: solute carrier family 45 member 2provided by HGNC
Primary source: HGNC:HGNC:16472
See related: Ensembl:ENSG00000164175 MIM:606202; AllianceGenome:HGNC:16472
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: 1A1; AIM1; MATP; OCA4; SHEP5
Summary: This gene encodes a transporter protein that mediates melanin synthesis. The protein is expressed in a high percentage of melanoma cell lines. Mutations in this gene are a cause of oculocutaneous albinism type 4, and polymorphisms in this gene are associated with variations in skin and hair color. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 5p13.2

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (33944623..33984693, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (34066546..34106612, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (33944728..33984798, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Native American genetic ancestry and pigmentation allele contributions to skin color in a Caribbean population.
Title: Native American genetic ancestry and pigmentation allele contributions to skin color in a Caribbean population.
Oncogenic Activity of Solute Carrier Family 45 Member 2 and Alpha-Methylacyl-Coenzyme A Racemase Gene Fusion Is Mediated by Mitogen-Activated Protein Kinase.
Title: Oncogenic Activity of Solute Carrier Family 45 Member 2 and Alpha-Methylacyl-Coenzyme A Racemase Gene Fusion Is Mediated by Mitogen-Activated Protein Kinase.
Homozygous promoter variant of SLC45A2 causes diverse hair color and patterns.
Title: Homozygous promoter variant of SLC45A2 causes diverse hair color and patterns.
SLC45A2 protein stability and regulation of melanosome pH determine melanocyte pigmentation.
Title: SLC45A2 protein stability and regulation of melanosome pH determine melanocyte pigmentation.
A novel deletion mutation c.579delG [p.(Gly194Valfs*7)] in the SLC45A2 gene, predicted to be pathogenic and to result in both frameshift and premature termination of the MATP chain, was identified in a family.
Title: Whole exome sequencing identifies a novel pathogenic variation [p.(Gly194valfs*7)] in SLC45A2 in the homozygous state in multiple members of a family with oculocutaneous albinism in southern India.
Study in two unrelated oculocutaneous albinism (OCA)-suspected Japanese female patients concluded that the homozygous 4-bp deletion variant (rs984225803) in the promoter region of SLC45A2 caused the OCA-like phenotype.
Title: Impact of a 4-bp deletion variant (rs984225803) in the promoter region of SLC45A2 on color variation among a Japanese population.
AIM1 first Greek motif g1 is required for the main physiological functions of AIM1.AIM1 interaction with beta-actin.
Title: Purification and Functional Characterization of the C-Terminal Domain of the β-Actin-Binding Protein AIM1 In Vitro.
Study confirmed a significant role for IRF4 rs12203592 and SLC45A2 rs16891982 in the risk of cutaneous squamous cell carcinoma development in organ transplant recipients.
Title: IRF4 Polymorphism Is Associated with Cutaneous Squamous Cell Carcinoma in Organ Transplant Recipients: A Pigment-Independent Phenomenon.
our study demonstrates the feasibility of using tandem MS as a means of discovering shared immunogenic tumor-associated epitopes and identifies SLC45A2 as a promising immunotherapeutic target for melanoma with high tumor selectivity and reduced potential for autoimmune toxicity
Title: SLC45A2: A Melanoma Antigen with High Tumor Selectivity and Reduced Potential for Autoimmune Toxicity.
Evaluating the influence of haplotypes of 12 SNPs within SLC45A2 in the determination of eye, hair and skin pigmentation in a highly admixed population sample and comparing their frequencies with the ones found in data retrieved from the 1000 Genomes Project. Results emphasize the role played by haplotypes at SLC45A2 in the determination of pigmentation and reinforce the relevance of SNP L374F in human pigmentation.
Title: Haplotypes from the SLC45A2 gene are associated with the presence of freckles and eye, hair and skin pigmentation in Brazil.

Submit: New GeneRIF Correction See all GeneRIFs (54)

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
Oculocutaneous albinism type 4 MedGen: C1847836 OMIM: 606574 GeneReviews: Oculocutaneous Albinism Type 4, Oculocutaneous Albinism and Ocular Albinism Overview	Compare labs
Skin/hair/eye pigmentation, variation in, 5 MedGen: C2673584 OMIM: 227240 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genomewide association study of skin pigmentation in a South Asian population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies three new melanoma susceptibility loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of tanning phenotype in a population of European ancestry. EBI GWAS Catalog EBI GWAS CatalogPubMed
Web-based, participant-driven studies yield novel genetic associations for common traits. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-56588 (e-PCR)
- UniSTS:52742

STS-N23139 (e-PCR)
- UniSTS:64006

RH16380 (e-PCR)
- UniSTS:12812

SHGC-36018 (e-PCR)
- UniSTS:76152

SHGC-132566 (e-PCR)
- UniSTS:173950

SHGC-147068 (e-PCR)
- UniSTS:172740

D5S1430 (e-PCR)
- UniSTS:181704

D5S1430 (e-PCR)
- UniSTS:58854

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables glucose:proton symporter activity	ISS Inferred from Sequence or Structural Similarity more info
enables sucrose:proton symporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables sucrose:proton symporter activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in developmental pigmentation	ISS Inferred from Sequence or Structural Similarity more info
involved_in glucose transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in lysosomal lumen pH elevation	IDA Inferred from Direct Assay more info	PubMed
involved_in lysosomal lumen pH elevation	ISS Inferred from Sequence or Structural Similarity more info
involved_in melanin biosynthetic process from tyrosine	IDA Inferred from Direct Assay more info	PubMed
involved_in melanin biosynthetic process from tyrosine	ISS Inferred from Sequence or Structural Similarity more info
involved_in sucrose transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in visual perception	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in melanosome membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: membrane-associated transporter protein

Names: antigen in melanoma 1; melanoma antigen AIM1; oculocutaneous albinism type 4; protein AIM-1; underwhite

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

NG_011691.3 RefSeqGene

Range

5000..45070

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001012509.4 → NP_001012527.2 membrane-associated transporter protein isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 3' UTR and coding region compared to variant 1. The resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a.

Source sequence(s)

AC139777, AC139783

Consensus CDS

CCDS43308.1

UniProtKB/TrEMBL

A0A076YGN1

Related

ENSP00000371534.3, ENST00000382102.7

Conserved Domains (1) summary

cd17313
Location:35 → 453

MFS_SLC45_SUC; Solute carrier family 45 and similar sugar transporters of the Major Facilitator Superfamily of transporters
NM_001297417.4 → NP_001284346.2 membrane-associated transporter protein isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (3) has multiple differences, which result in a translational frameshift and an earlier translation termination as well as a novel 3' UTR, compared to variant 1. The resulting isoform (c) is shorter and has a distinct C-terminus, compared to isoform a.

Source sequence(s)

AC139777, AC139783

Consensus CDS

CCDS75232.1

UniProtKB/TrEMBL

D6RGY6

Related

ENSP00000421100.1, ENST00000509381.1

Conserved Domains (1) summary

cd06174
Location:34 → 157

MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
NM_016180.5 → NP_057264.4 membrane-associated transporter protein isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (a).

Source sequence(s)

AC139777, AC139783

Consensus CDS

CCDS3901.1

UniProtKB/Swiss-Prot

Q6P2P0, Q9BTM3, Q9UMX9

UniProtKB/TrEMBL

A0A076YGN1, A0A076YIB8

Related

ENSP00000296589.4, ENST00000296589.9

Conserved Domains (1) summary

TIGR01301
Location:31 → 449

GPH_sucrose; GPH family sucrose/H+ symporter

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

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

33944623..33984693 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047417259.1 → XP_047273215.1 membrane-associated transporter protein isoform X1
XM_047417260.1 → XP_047273216.1 membrane-associated transporter protein isoform X2

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

NT_187551.1 Reference GRCh38.p14 ALT_REF_LOCI_1

Range

145945..155829 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060929.1 Alternate T2T-CHM13v2.0

Range

34066546..34106612 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054352715.1 → XP_054208690.1 membrane-associated transporter protein isoform X1
XM_054352716.1 → XP_054208691.1 membrane-associated transporter protein isoform X2