SLC13A4

solute carrier family 13 member 4, the group of Solute carrier family 13

Basic information

Region (hg38): 7:135681230-135729258

Links

ENSG00000164707 ∙ NCBI:26266 ∙ OMIM:604309 ∙ HGNC:15827 ∙ Uniprot:Q9UKG4 ∙ 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 SLC13A4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC13A4 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			23	3		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	3	0

Variants in SLC13A4

This is a list of pathogenic ClinVar variants found in the SLC13A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-135681573-T-C		not specified	Uncertain significance (May 25, 2022)
7-135681642-T-C		not specified	Uncertain significance (Jan 30, 2024)
7-135681659-T-C		not specified	Uncertain significance (Apr 28, 2023)
7-135684126-T-A		not specified	Uncertain significance (Sep 17, 2021)
7-135684137-T-C		not specified	Uncertain significance (Mar 29, 2022)
7-135684159-C-T		not specified	Uncertain significance (Apr 15, 2024)
7-135684162-T-C		not specified	Uncertain significance (Aug 09, 2021)
7-135684230-G-A		not specified	Uncertain significance (Dec 14, 2021)
7-135685655-T-G		not specified	Uncertain significance (Oct 12, 2022)
7-135691238-A-G		not specified	Uncertain significance (Oct 05, 2023)
7-135691259-A-G		not specified	Uncertain significance (Oct 25, 2022)
7-135691635-G-A		not specified	Uncertain significance (Jan 10, 2023)
7-135692381-C-T		not specified	Uncertain significance (Jul 27, 2022)
7-135692420-G-A		not specified	Uncertain significance (Apr 13, 2022)
7-135694189-G-C		not specified	Likely benign (May 22, 2023)
7-135695393-T-C		not specified	Uncertain significance (Jul 12, 2022)
7-135701717-G-A		not specified	Uncertain significance (Oct 10, 2023)
7-135702847-C-T		not specified	Likely benign (Feb 10, 2022)
7-135706182-C-T		not specified	Uncertain significance (Mar 15, 2023)
7-135706215-C-T		not specified	Uncertain significance (Jun 29, 2023)
7-135706232-G-A		not specified	Uncertain significance (Sep 22, 2022)
7-135706283-A-G		not specified	Uncertain significance (Feb 07, 2023)
7-135708147-C-G		not specified	Uncertain significance (Mar 22, 2022)
7-135708147-C-T		not specified	Uncertain significance (Dec 06, 2022)
7-135708205-C-A		not specified	Uncertain significance (Dec 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC13A4	protein_coding	protein_coding	ENST00000354042	16	48022

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.816	0.184	125729	0	18	125747	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.01	256	364	0.703	0.0000204	4089
Missense in Polyphen		110	169.67	0.6483		1904
Synonymous	-0.0397	161	160	1.00	0.0000105	1283
Loss of Function	4.26	6	32.0	0.188	0.00000154	352

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000140	0.000139
European (Non-Finnish)	0.0000710	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000666	0.0000653
Other	0.000177	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sodium/sulfate cotransporter that mediates sulfate reabsorption in the high endothelial venules (HEV). {ECO:0000269|PubMed:10535998, ECO:0000269|PubMed:15607730}.
• Pathway: Bile salt and organic anion SLC transporters;Sodium-coupled sulphate, di- and tri-carboxylate transporters;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Methionine and cysteine metabolism (Consensus)

Recessive Scores

• pRec: 0.161

Intolerance Scores

• loftool: 0.379
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.72

Haploinsufficiency Scores

• pHI: 0.110
• hipred: Y
• hipred_score: 0.728
• ghis: 0.425

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.129

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc13a4
• Phenotype: embryo 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); vision/eye phenotype; digestive/alimentary phenotype; skeleton phenotype; homeostasis/metabolism 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); growth/size/body region phenotype; craniofacial phenotype

Gene ontology

• Biological process: sodium ion transport;sulfate transport;citrate transport;succinate transmembrane transport;sulfate transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;integral component of membrane
• Molecular function: citrate transmembrane transporter activity;succinate transmembrane transporter activity;sodium:sulfate symporter activity;sodium:dicarboxylate symporter activity