GeneBe

SLC45A2

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

Basic information

Region (hg38): 5:33944623-33984693

Previous symbols: [ "MATP" ]

Links

ENSG00000164175 ∙ NCBI:51151 ∙ OMIM:606202 ∙ HGNC:16472 ∙ Uniprot:Q9UMX9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • oculocutaneous albinism type 4 (Definitive), mode of inheritance: AR
  • oculocutaneous albinism type 4 (Supportive), mode of inheritance: AR
  • oculocutaneous albinism type 4 (Definitive), mode of inheritance: AR
  • oculocutaneous albinism type 4 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Oculocutaneous albinism, type IV; Skin/hair/eye pigmentation 5AD/ARGeneralVariants associated with Skin/hair/eye pigmentation 5 are associated with a slight increased risk of skin cancer, but clinical applicability is otherwise unclearDermatologic; Ophthalmologic11574907; 14722913; 14961451; 15714523; 17358008; 17999355; 19578363
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

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC45A2 gene.

  • not_provided (516 variants)
  • Oculocutaneous_albinism_type_4 (112 variants)
  • Inborn_genetic_diseases (55 variants)
  • SKIN/HAIR/EYE_PIGMENTATION_5,_BLACK/NONBLACK_HAIR (35 variants)
  • not_specified (32 variants)
  • SLC45A2-related_disorder (19 variants)
  • Oculocutaneous_albinism (1 variants)
  • Thrombocytopenia (1 variants)
  • Abnormal_bleeding (1 variants)
  • Nonsyndromic_Oculocutaneous_Albinism (1 variants)
  • Albinism_or_congenital_nystagmus (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC45A2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016180.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
8
clinvar
179
clinvar
1
clinvar
 189
missense
9
clinvar
38
clinvar
205
clinvar
4
clinvar
1
clinvar
 257
nonsense
17
clinvar
3
clinvar
 20
start loss
1
3
 4
frameshift
30
clinvar
11
clinvar
 41
splice donor/acceptor (+/-2bp)
5
clinvar
4
clinvar
 9
Total 63 59 213 183 2

Highest pathogenic variant AF is 0.000449748

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLC45A2protein_codingprotein_codingENST00000296589 740115
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.000001660.87212561801301257480.000517
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.113502961.180.00001783442
Missense in Polyphen146126.791.15151450
Synonymous-1.281431251.150.000008571100
Loss of Function1.531219.20.6238.41e-7242

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0009350.000934
Ashkenazi Jewish0.0006940.000695
East Asian0.0001630.000163
Finnish0.0003230.000323
European (Non-Finnish)0.0007840.000783
Middle Eastern0.0001630.000163
South Asian0.00003270.0000327
Other0.0003260.000326

dbNSFP

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.;
Pathway
Prader-Willi and Angelman Syndrome;Metabolism of amino acids and derivatives;Metabolism;Melanin biosynthesis (Consensus)

Recessive Scores

pRec
0.585

Intolerance Scores

loftool
0.0952
rvis_EVS
-0.98
rvis_percentile_EVS
8.85

Haploinsufficiency Scores

pHI
0.110
hipred
N
hipred_score
0.251
ghis
0.425

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.204

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyHighMediumHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Slc45a2
Phenotype
integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; pigmentation phenotype; vision/eye phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype;

Zebrafish Information Network

Gene name
slc45a2
Affected structure
eye photoreceptor cell
Phenotype tag
abnormal
Phenotype quality
apoptotic

Gene ontology

Biological process
visual perception;sucrose transport;melanin biosynthetic process;developmental pigmentation;response to stimulus
Cellular component
membrane;integral component of membrane;melanosome membrane
Molecular function
sucrose:proton symporter activity