SLC24A1

solute carrier family 24 member 1, the group of Solute carrier family 24

Basic information

Region (hg38): 15:65611366-65660995

Links

ENSG00000074621 ∙ NCBI:9187 ∙ OMIM:603617 ∙ HGNC:10975 ∙ Uniprot:O60721 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital stationary night blindness (Supportive), mode of inheritance: AD
• congenital stationary night blindness 1D (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Night blindness, congenital stationary, type 1D	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	Ophthalmologic	20850105

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC24A1 gene.

• not provided (25 variants)
• Congenital stationary night blindness 1D (2 variants)
• SLC24A1-related disorder (2 variants)
• Retinitis pigmentosa (1 variants)
• Congenital stationary night blindness autosomal dominant 2 (1 variants)
• Retinal dystrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC24A1 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			7	124	6	137
missense			337	5	4	346
nonsense	12	1	1			14
start loss			2			2
frameshift	13	2	3			18
inframe indel			24			24
splice donor/acceptor (+/-2bp)		1	1			2
splice region			9	6		15
non coding			30	44	19	93
Total	25	4	405	173	29

Highest pathogenic variant AF is 0.000145

Variants in SLC24A1

This is a list of pathogenic ClinVar variants found in the SLC24A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-65621944-G-A		Congenital stationary night blindness 1D	Likely benign (Jan 12, 2018)
15-65622037-T-C		Congenital stationary night blindness 1D	Benign (Jan 13, 2018)
15-65622055-C-T		Congenital stationary night blindness 1D	Likely benign (Jan 12, 2018)
15-65622058-G-A		Congenital stationary night blindness 1D	Uncertain significance (Jan 12, 2018)
15-65622102-G-A		Congenital stationary night blindness 1D	Uncertain significance (Jan 12, 2018)
15-65623968-C-T		Congenital stationary night blindness 1D	Likely benign (Jan 13, 2018)
15-65624008-A-G		Congenital stationary night blindness 1D	Uncertain significance (Jan 13, 2018)
15-65624032-T-C		Congenital stationary night blindness 1D	Uncertain significance (Jan 12, 2018)
15-65624081-A-G			Uncertain significance (Sep 30, 2019)
15-65624082-T-C		Congenital stationary night blindness 1D	Uncertain significance (Jan 12, 2018)
15-65624106-C-T			Uncertain significance (Oct 17, 2022)
15-65624107-G-C			Benign (Dec 11, 2023)
15-65624121-T-G		Retinal dystrophy	Pathogenic (Jan 01, 2018)
15-65624126-C-T			Uncertain significance (Jun 04, 2022)
15-65624127-G-A		Congenital stationary night blindness 1D	Uncertain significance (Oct 04, 2022)
15-65624135-C-T		Inborn genetic diseases • Retinal dystrophy	Uncertain significance (Dec 02, 2022)
15-65624137-G-A			Likely benign (May 13, 2022)
15-65624141-C-A			Uncertain significance (Aug 31, 2021)
15-65624142-A-G			Uncertain significance (Sep 01, 2022)
15-65624143-T-C			Likely benign (Jul 26, 2022)
15-65624148-G-T		Inborn genetic diseases	Uncertain significance (Jul 22, 2024)
15-65624150-C-T		Congenital Stationary Night Blindness, Recessive • Inborn genetic diseases	Uncertain significance (Oct 14, 2023)
15-65624151-G-A			Uncertain significance (Sep 06, 2022)
15-65624154-T-G			Uncertain significance (Aug 31, 2021)
15-65624156-C-T		Congenital stationary night blindness 1D	Uncertain significance (Sep 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC24A1	protein_coding	protein_coding	ENST00000261892	9	49630

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000922	1.00	124632	0	108	124740	0.000433

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.80	471	595	0.792	0.0000314	7187
Missense in Polyphen		76	104.26	0.72898		1242
Synonymous	0.777	211	226	0.934	0.0000130	2200
Loss of Function	3.65	14	38.4	0.364	0.00000198	469

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00121	0.00119
Ashkenazi Jewish	0.0000994	0.0000994
East Asian	0.000175	0.000166
Finnish	0.0000930	0.0000928
European (Non-Finnish)	0.000532	0.000522
Middle Eastern	0.000175	0.000166
South Asian	0.000398	0.000327
Other	0.000331	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Critical component of the visual transduction cascade, controlling the calcium concentration of outer segments during light and darkness. Light causes a rapid lowering of cytosolic free calcium in the outer segment of both retinal rod and cone photoreceptors and the light-induced lowering of calcium is caused by extrusion via this protein which plays a key role in the process of light adaptation. Transports 1 Ca(2+) and 1 K(+) in exchange for 4 Na(+). {ECO:0000269|PubMed:10608890}.
• Disease: DISEASE: Night blindness, congenital stationary, 1D (CSNB1D) [MIM:613830]: An autosomal recessive form of congenital stationary night blindness, a non-progressive retinal disorder characterized by impaired night vision. CSNB1D is characterized by a Riggs type of electroretinogram (proportionally reduced a- and b-waves). Patients have visual acuity within the normal range and no symptoms of myopia and/or nystagmus. {ECO:0000269|PubMed:20850105}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Phototransduction - Homo sapiens (human);Signaling by GPCR;Signal Transduction;Sodium/Calcium exchangers;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Visual signal transduction: Rods;G alpha (i) signalling events;Activation of the phototransduction cascade;The phototransduction cascade;Visual phototransduction;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.0954

Intolerance Scores

• loftool: 0.875
• rvis_EVS: -0.57
• rvis_percentile_EVS: 19.04

Haploinsufficiency Scores

• pHI: 0.493
• hipred: N
• hipred_score: 0.270
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.667

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc24a1
• 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

Gene ontology

• Biological process: ion transport;calcium ion transport;cellular calcium ion homeostasis;visual perception;response to light intensity;sodium ion transmembrane transport;long-term synaptic potentiation;long-term synaptic depression;calcium ion transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;membrane;outer membrane
• Molecular function: calcium channel activity;protein binding;calcium, potassium:sodium antiporter activity;symporter activity