GeneBe

SLC45A2

protein-coding

solute carrier family 45 member 2, the group of Solute carrier family 45

Gene 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]

Previous symbols:
  • MATP

MANE transcript

NM_016180.5

Inheritance

AR, AD

ClinVar variants

P:145U:224B:194

Top phenotype

Oculocutaneous albinism, type IV; Skin/hair/eye pigmentation 5

gnomAD constraint

pLI —, LoF o/e 0.62

Max pathogenic AF

—

Genomic locus

chr5:33,944,623-33,984,693

External References & Databases

Ensembl (ENSG00000164175)NCBI Gene (51151)OMIM (606202)HGNC:16472GenCCUniProt (Q9UMX9)AlphaFoldClinVar (SLC45A2)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~40.1 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

oculocutaneous albinism type 4DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0011683

Submitter: Ambry Genetics

oculocutaneous albinism type 4STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011683

Submitter: Labcorp Genetics (formerly Invitae)

oculocutaneous albinism type 4STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011683

Submitter: PanelApp Australia

oculocutaneous albinism type 4DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0011683

Submitter: G2P

oculocutaneous albinism type 4SUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0011683

Submitter: Orphanet

Clinical Genomic Database (CGD)

Oculocutaneous albinism, type IV; Skin/hair/eye pigmentation 5AD/AR

Manifestation: Dermatologic; Ophthalmologic

Intervention: General

Rationale: Variants associated with Skin/hair/eye pigmentation 5 are associated with a slight increased risk of skin cancer, but clinical applicability is otherwise unclear

Comments: In Oculocutaneous albinism, type IV, Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 11574907; 14722913; 14961451; 15714523; 17358008; 17999355; 19578363Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC45A2 variants in ClinVar

11 Conditions Cataloged
not providedTotal: 541
Oculocutaneous albinism type 4Total: 123
not specifiedTotal: 78
Inborn genetic diseasesTotal: 63
SLC45A2-related disorderTotal: 58
SKIN/HAIR/EYE PIGMENTATION 5, BLACK/NONBLACK HAIRTotal: 48
ThrombocytopeniaTotal: 1
Abnormal bleedingTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016180.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
9
clinvar
187
clinvar
 196
missense
10
clinvar
52
clinvar
215
clinvar
7
clinvar
 284
nonsense
18
clinvar
5
clinvar
 23
start loss
1
clinvar
3
clinvar
 4
frameshift
31
clinvar
16
clinvar
 47
splice donor/acceptor (+/-2bp)
5
clinvar
4
clinvar
 9
Total65802241940563

Highest pathogenic variant AF is 0.0004497478

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_016180.5RefSeqNP_057264.47MANE Select
ENST00000296589.9EnsemblENSP00000296589.47MANE Select
NM_001012509.4RefSeqNP_001012527.26Standard
NM_001297417.4RefSeqNP_001284346.24Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
slc45a2Danio rerio

Structure: eye photoreceptor cell

Quality: apoptotic

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Prader-Willi and Angelman Syndrome
  • Metabolism of amino acids and derivatives
  • Metabolism
  • Melanin biosynthesis

Biological Process

  • visual perception
  • sucrose transport
  • melanin biosynthetic process
  • developmental pigmentation
  • response to stimulus

Molecular Function

  • sucrose:proton symporter activity

Cellular Component

  • membrane
  • integral component of membrane
  • melanosome membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000296589
Coding exons
7
Length
40115
Individuals with no LoFs
125618
Homozygous LoFs
0
Heterozygous LoFs
130
Defined
125748
p
0.000517
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-1.113502961.180.00001783442
Missense (PolyPhen)146126.791.15151450
Synonymous-1.281431251.150.000008571100
Loss of Function1.531219.20.6238.41e-7242

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000620.00062rare
Latino/Admixed American0.000320.00032rare
Ashkenazi Jewish0.000690.00069rare
East Asian0.000160.00016rare
Finnish0.000320.00032rare
European (Non-Finnish)0.000780.00078rare
South Asian0.0000330.000033rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Melanocyte differentiation antigen. May transport substances required for melanin biosynthesis (By similarity). {ECO:0000250}.;
Disease
DISEASE: Albinism, oculocutaneous, 4 (OCA4) [MIM:606574]: A disorder of pigmentation characterized by reduced biosynthesis of melanin in the skin, hair and eyes. Patients show reduced or lacking pigmentation associated with classic albinism ocular abnormalities, including decreased visual acuity, macular hypoplasia, optic dysplasia, atypical choroidal vessels, and nystagmus. {ECO:0000269|PubMed:11574907, ECO:0000269|PubMed:14722913, ECO:0000269|PubMed:14961451, ECO:0000269|PubMed:15656822, ECO:0000269|PubMed:17768386, ECO:0000269|PubMed:19865097, ECO:0000269|PubMed:23504663}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.585

Intolerance Scores

LoFtool
0.0952
RVIS EVS
-0.98
RVIS percentile EVS
8.85

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.204

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyHighMediumHigh
CancerHighHighHigh
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