SLC45A2

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

Basic information

Region (hg38): 5:33944622-33984693

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Oculocutaneous albinism, type IV; Skin/hair/eye pigmentation 5	AD/AR	General	Variants associated with Skin/hair/eye pigmentation 5 are associated with a slight increased risk of skin cancer, but clinical applicability is otherwise unclear	Dermatologic; Ophthalmologic	11574907; 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 (392 variants)
• Oculocutaneous albinism type 4 (65 variants)
• not specified (15 variants)
• Inborn genetic diseases (12 variants)
• Oculocutaneous albinism type 4;Skin/hair/eye pigmentation, variation in, 5 (6 variants)
• SLC45A2-related condition (4 variants)
• Skin/hair/eye pigmentation, variation in, 5;Oculocutaneous albinism type 4 (3 variants)
• Skin/hair/eye pigmentation, variation in, 5 (2 variants)
• Thrombocytopenia;Abnormal bleeding (1 variants)
• Oculocutaneous albinism (1 variants)
• Nonsyndromic Oculocutaneous Albinism (1 variants)
• Malignant melanoma of skin (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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			6	85	1	92
missense	11	12	163	13	3	202
nonsense	10	2				12
start loss		3				3
frameshift	15	2	1			18
inframe indel		1	5			6
splice donor/acceptor (+/-2bp)	1	1				2
splice region			2	10		12
non coding	2		4	34	15	55
Total	39	21	179	132	19

Highest pathogenic variant AF is 0.000210

Variants in SLC45A2

This is a list of pathogenic ClinVar variants found in the SLC45A2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-33944624-T-G		Oculocutaneous albinism type 4	Likely benign (Jan 13, 2018)
5-33944647-C-T		Oculocutaneous albinism type 4	Uncertain significance (Jan 12, 2018)
5-33944649-T-C			Uncertain significance (Oct 17, 2022)
5-33944657-A-G			Likely benign (Mar 26, 2023)
5-33944662-T-C			Uncertain significance (Feb 21, 2022)
5-33944662-TAACA-T			Likely pathogenic (Jan 29, 2024)
5-33944666-A-AAAGAGAGC		Oculocutaneous albinism type 4	Uncertain significance (Apr 28, 2017)
5-33944669-G-A			Likely benign (Jul 16, 2023)
5-33944669-G-C			Likely benign (Aug 16, 2023)
5-33944671-G-A		Oculocutaneous albinism type 4;Skin/hair/eye pigmentation, variation in, 5	Uncertain significance (Apr 30, 2022)
5-33944674-C-T			Uncertain significance (Aug 06, 2022)
5-33944675-G-A			Likely benign (Aug 02, 2023)
5-33944675-G-C			Likely benign (Jan 09, 2024)
5-33944686-A-G			Likely pathogenic (Jan 31, 2024)
5-33944691-A-G			Uncertain significance (May 15, 2022)
5-33944693-C-A			Likely benign (Dec 29, 2023)
5-33944693-C-G			Likely benign (May 06, 2021)
5-33944702-C-T			Likely benign (Nov 20, 2023)
5-33944701-C-CCGCAGA			Uncertain significance (Oct 22, 2021)
5-33944703-G-T			Pathogenic (Jan 16, 2024)
5-33944708-C-T		Oculocutaneous albinism type 4 • SLC45A2-related disorder	Conflicting classifications of pathogenicity (Jan 09, 2024)
5-33944709-G-A		Nonsyndromic Oculocutaneous Albinism	Conflicting classifications of pathogenicity (Feb 05, 2022)
5-33944709-G-T			Pathogenic (Jan 20, 2024)
5-33944713-T-C			Uncertain significance (Jul 03, 2023)
5-33944719-C-A			Uncertain significance (Oct 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC45A2	protein_coding	protein_coding	ENST00000296589	7	40115

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000166	0.872	125618	0	130	125748	0.000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.11	350	296	1.18	0.0000178	3442
Missense in Polyphen		146	126.79	1.1515		1450
Synonymous	-1.28	143	125	1.15	0.00000857	1100
Loss of Function	1.53	12	19.2	0.623	8.41e-7	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000935	0.000934
Ashkenazi Jewish	0.000694	0.000695
East Asian	0.000163	0.000163
Finnish	0.000323	0.000323
European (Non-Finnish)	0.000784	0.000783
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
Other	0.000326	0.000326

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	High	Medium	High
Cancer	High	High	High

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