SLC24A2

solute carrier family 24 member 2, the group of Solute carrier family 24

Basic information

Region (hg38): 9:19507451-19789037

Links

ENSG00000155886 ∙ NCBI:25769 ∙ OMIM:609838 ∙ HGNC:10976 ∙ Uniprot:Q9UI40 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC24A2 gene.

• Inborn genetic diseases (23 variants)
• not provided (1 variants)
• Abnormal retinal morphology (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC24A2 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						0
missense			21	3		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	3	0

Variants in SLC24A2

This is a list of pathogenic ClinVar variants found in the SLC24A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-19516164-C-T		not specified	Uncertain significance (Nov 15, 2021)
9-19516167-G-T		not specified	Uncertain significance (Nov 30, 2021)
9-19516290-C-T		not specified	Uncertain significance (Feb 14, 2023)
9-19516337-T-C		Abnormal retinal morphology	Benign/Likely benign (Jun 20, 2017)
9-19516374-C-T		not specified	Likely benign (Feb 07, 2023)
9-19521029-A-C		not specified	Uncertain significance (Aug 12, 2021)
9-19528071-A-C		not specified	Uncertain significance (Jan 20, 2023)
9-19528079-G-C		not specified	Uncertain significance (Jul 14, 2021)
9-19528120-G-C		not specified	Uncertain significance (Jun 09, 2022)
9-19550148-C-T		not specified	Uncertain significance (Jan 02, 2024)
9-19550265-C-T		not specified	Uncertain significance (Dec 26, 2023)
9-19573370-A-G		not specified	Uncertain significance (Apr 28, 2023)
9-19573398-C-T		not specified	Uncertain significance (Jul 30, 2023)
9-19573442-C-G		not specified	Uncertain significance (Jan 04, 2024)
9-19576927-C-T		not specified	Uncertain significance (Feb 06, 2024)
9-19576950-C-T		not specified	Uncertain significance (Jun 29, 2022)
9-19619590-C-T		not specified	Uncertain significance (Dec 14, 2023)
9-19619682-C-T		not specified	Uncertain significance (Dec 22, 2023)
9-19619685-G-A		not specified	Uncertain significance (May 11, 2022)
9-19785957-C-T		not specified	Uncertain significance (Apr 05, 2023)
9-19785980-C-T		not specified	Uncertain significance (May 24, 2023)
9-19786091-T-C		not specified	Uncertain significance (Jan 10, 2023)
9-19786247-G-A		not specified	Uncertain significance (Oct 05, 2023)
9-19786260-C-T		not specified	Uncertain significance (Jul 14, 2021)
9-19786272-C-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC24A2	protein_coding	protein_coding	ENST00000341998	10	279477

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00571	0.994	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.211	365	354	1.03	0.0000195	4352
Missense in Polyphen		77	113.86	0.67627		1452
Synonymous	-2.02	163	133	1.22	0.00000838	1294
Loss of Function	3.26	9	27.4	0.328	0.00000141	323

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000118	0.000118
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

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(+).
• Pathway: Sodium/Calcium exchangers;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Visual signal transduction: Cones (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.449
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.73

Haploinsufficiency Scores

• pHI: 0.265
• hipred: Y
• hipred_score: 0.554
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.219

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc24a2
• Phenotype: homeostasis/metabolism 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

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