SLC24A5

solute carrier family 24 member 5, the group of Solute carrier family 24

Basic information

Region (hg38): 15:48120989-48142672

Links

ENSG00000188467 ∙ NCBI:283652 ∙ OMIM:609802 ∙ HGNC:20611 ∙ Uniprot:Q71RS6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• oculocutaneous albinism type 6 (Strong), mode of inheritance: AR
• oculocutaneous albinism type 6 (Supportive), mode of inheritance: AR
• oculocutaneous albinism type 6 (Definitive), mode of inheritance: AR
• oculocutaneous albinism type 7 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Albinism, oculocutaneous, type VI	AR	General	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	Dermatologic; Ophthalmologic	23364476
Variants may also influence relative pigmentation in the general population

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC24A5 gene.

• not provided (190 variants)
• Inborn genetic diseases (9 variants)
• not specified (5 variants)
• Oculocutaneous albinism type 6 (4 variants)
• Oculocutaneous albinism (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC24A5 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				34	1	35
missense	1	1	94	5	1	102
nonsense	7	1	1			9
start loss						0
frameshift	10	1	1			12
inframe indel			2			2
splice donor/acceptor (+/-2bp)		7				7
splice region	1		4	2	1	8
non coding			1	15		16
Total	18	10	99	54	2

Highest pathogenic variant AF is 0.0000461

Variants in SLC24A5

This is a list of pathogenic ClinVar variants found in the SLC24A5 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-48121054-A-G			Uncertain significance (Sep 27, 2022)
15-48121060-G-A			Uncertain significance (Apr 29, 2022)
15-48121062-CCAAACATGGG-C			Pathogenic (Jul 25, 2022)
15-48121068-A-C			Likely benign (Nov 23, 2023)
15-48121070-G-A			Pathogenic (Jun 28, 2022)
15-48121072-G-C			Likely benign (Nov 28, 2023)
15-48121073-C-T			Uncertain significance (Mar 27, 2022)
15-48121074-G-A			Likely benign (Oct 30, 2023)
15-48121092-C-T			Likely benign (Nov 21, 2023)
15-48121093-G-C			Uncertain significance (Jul 19, 2022)
15-48121099-C-A			Uncertain significance (Oct 28, 2022)
15-48121109-C-G			Uncertain significance (Jul 19, 2022)
15-48121114-C-T			Uncertain significance (Nov 08, 2022)
15-48121117-C-T			Likely benign (Sep 10, 2023)
15-48121126-T-C			Uncertain significance (Feb 06, 2022)
15-48121131-G-A			Likely benign (May 07, 2022)
15-48121136-C-T			Uncertain significance (Nov 01, 2022)
15-48121139-TG-T			Pathogenic (Mar 23, 2022)
15-48121146-A-G			Likely benign (Nov 13, 2023)
15-48121159-G-T			Uncertain significance (Mar 09, 2022)
15-48121166-G-A			Likely pathogenic (Jul 03, 2022)
15-48121173-G-A			Likely benign (Sep 06, 2022)
15-48121178-T-G			Likely benign (Aug 17, 2023)
15-48121182-G-A			Likely benign (Apr 12, 2022)
15-48121853-A-T			Uncertain significance (Jan 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC24A5	protein_coding	protein_coding	ENST00000341459	9	21701

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.15e-10	0.379	125609	1	133	125743	0.000533

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.317	256	271	0.946	0.0000132	3232
Missense in Polyphen		59	70.714	0.83435		855
Synonymous	-0.0599	101	100	1.01	0.00000525	1009
Loss of Function	0.974	17	21.9	0.775	9.23e-7	289

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000448	0.000448
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000834	0.000832
European (Non-Finnish)	0.000755	0.000747
Middle Eastern	0.000163	0.000163
South Asian	0.000491	0.000457
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cation exchanger involved in pigmentation, possibly by participating in ion transport in melanosomes. Predominant sodium- Calcium exchanger in melanocytes. Probably transports 1 Ca(2+) and 1 K(+) to the melanosome in exchange for 4 cytoplasmic Na(+). {ECO:0000269|PubMed:16357253, ECO:0000269|PubMed:18166528}.
• Disease: DISEASE: Albinism, oculocutaneous, 6 (OCA6) [MIM:113750]: A disorder characterized by a reduction or complete loss of melanin in the skin, hair and eyes. Patients show reduced or lacking pigmentation often accompanied by eye symptoms such as photophobia, strabismus, moderate to severe visual impairment, and nystagmus. {ECO:0000269|PubMed:23364476}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Sodium/Calcium exchangers;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.194

Intolerance Scores

• loftool: 0.909
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.2

Haploinsufficiency Scores

• pHI: 0.170
• hipred: N
• hipred_score: 0.250
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.135

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc24a5
• Phenotype: craniofacial phenotype; homeostasis/metabolism phenotype; growth/size/body region 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); pigmentation phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: slc24a5
• Affected structure: melanocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased pigmentation

Gene ontology

• Biological process: ion transport;potassium ion transport;cellular calcium ion homeostasis;melanocyte differentiation;ion transmembrane transport;sodium ion transmembrane transport;negative regulation of melanin biosynthetic process;response to stimulus;calcium ion transmembrane transport
• Cellular component: trans-Golgi network;integral component of membrane;trans-Golgi network membrane;melanosome
• Molecular function: calcium channel activity;calcium, potassium:sodium antiporter activity;symporter activity