SLC4A7

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

Basic information

Region (hg38): 3:27372723-27484420

Previous symbols: [ "SLC4A6" ]

Links

ENSG00000033867

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

Phenotypes

GenCC

Source: genCC

retinitis pigmentosa (Moderate), mode of inheritance: AR
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.

not_specified (94 variants)
SLC4A7-related_disorder (9 variants)
Retinal_dystrophy (4 variants)
not_provided (2 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. These statistics are base on transcript: NM_001321103.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	7 clinvar		10
missense			99 clinvar	3 clinvar		102
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	108	10	0

Loading clinvar variants...

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