SLC4A7

solute carrier family 4 member 7, the group of Solute carrier family 4

Basic information

Region (hg38): 3:27372720-27484420

Previous symbols: [ "SLC4A6" ]

Links

ENSG00000033867 ∙ NCBI:9497 ∙ OMIM:603353 ∙ HGNC:11033 ∙ Uniprot:Q9Y6M7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cone-rod dystrophy (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC4A7 gene.

• Inborn genetic diseases (31 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC4A7 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			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	1	0

Variants in SLC4A7

This is a list of pathogenic ClinVar variants found in the SLC4A7 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-27379241-A-G		SLC4A7-related disorder	Likely benign (Oct 15, 2019)
3-27383181-G-T		not specified	Uncertain significance (Oct 06, 2021)
3-27383241-G-A		not specified	Uncertain significance (Jan 09, 2024)
3-27385912-T-C		not specified	Uncertain significance (Apr 20, 2023)
3-27385974-T-G		not specified	Uncertain significance (Aug 01, 2022)
3-27389957-C-G		not specified	Uncertain significance (Dec 09, 2023)
3-27389997-C-G		not specified	Uncertain significance (Apr 20, 2023)
3-27390040-C-T		not specified	Uncertain significance (Feb 28, 2024)
3-27390047-A-G		not specified	Uncertain significance (Jul 07, 2022)
3-27391797-C-T		not specified	Uncertain significance (Dec 28, 2023)
3-27394592-G-A		not specified	Uncertain significance (Dec 18, 2023)
3-27394659-A-C		not specified	Uncertain significance (Oct 12, 2021)
3-27394726-A-G		not specified	Uncertain significance (Feb 17, 2022)
3-27394730-C-T		not specified	Likely benign (Dec 14, 2022)
3-27395024-C-T		not specified	Uncertain significance (Aug 04, 2022)
3-27395072-T-A		not specified	Uncertain significance (Dec 26, 2023)
3-27395104-T-C		SLC4A7-related disorder	Likely benign (Jun 24, 2019)
3-27397743-T-C		not specified	Likely benign (Jul 06, 2022)
3-27398285-A-G		SLC4A7-related disorder	Likely benign (Nov 19, 2019)
3-27400861-C-A		not specified	Uncertain significance (Feb 22, 2023)
3-27403173-T-C		not specified	Uncertain significance (Nov 30, 2022)
3-27403319-A-C			Uncertain significance (Oct 01, 2023)
3-27403370-G-C		not specified	Uncertain significance (Nov 15, 2021)
3-27404842-T-C		not specified	Uncertain significance (Nov 30, 2022)
3-27404955-T-C		not specified	Uncertain significance (Aug 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC4A7	protein_coding	protein_coding	ENST00000295736	25	111698

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.736	0.264	125706	0	40	125746	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.25	485	646	0.751	0.0000334	7919
Missense in Polyphen		168	301.12	0.55791		3718
Synonymous	-0.662	235	222	1.06	0.0000114	2361
Loss of Function	5.54	12	57.2	0.210	0.00000309	741

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000695	0.000691
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.000162	0.000158
Middle Eastern	0.000111	0.000109
South Asian	0.000172	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Electroneutral sodium- and bicarbonate-dependent cotransporter with a Na(+):HCO3(-) 1:1 stoichiometry. Regulates intracellular pH and may play a role in bicarbonate salvage in secretory epithelia. May also have an associated sodium channel activity. {ECO:0000269|PubMed:10347222, ECO:0000269|PubMed:12403779}.
• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Bicarbonate transporters (Consensus)

Recessive Scores

• pRec: 0.171

Intolerance Scores

• loftool: 0.469
• rvis_EVS: -0.97
• rvis_percentile_EVS: 8.96

Haploinsufficiency Scores

• pHI: 0.323
• hipred: N
• hipred_score: 0.476
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.511

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc4a7
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; skeleton phenotype; vision/eye 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); hearing/vestibular/ear phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: sodium ion transport;inorganic anion transport;bicarbonate transport;regulation of intracellular pH;auditory receptor cell development;anion transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;integral component of membrane;basolateral plasma membrane;apical plasma membrane;cytoplasmic vesicle;stereocilium;synapse
• Molecular function: inorganic anion exchanger activity;sodium:bicarbonate symporter activity