SLC13A1

solute carrier family 13 member 1, the group of Solute carrier family 13

Basic information

Region (hg38): 7:123113530-123199972

Links

ENSG00000081800 ∙ NCBI:6561 ∙ OMIM:606193 ∙ HGNC:10916 ∙ Uniprot:Q9BZW2 ∙ 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 SLC13A1 gene.

• Inborn genetic diseases (21 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC13A1 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				2		2
missense			19	2	2	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	19	4	3

Variants in SLC13A1

This is a list of pathogenic ClinVar variants found in the SLC13A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-123115555-G-A		not specified	Uncertain significance (Oct 12, 2022)
7-123115579-A-T		not specified	Uncertain significance (Nov 09, 2022)
7-123117451-A-AT			Benign (Aug 15, 2019)
7-123117508-A-G		not specified	Uncertain significance (May 23, 2023)
7-123117520-G-T		not specified	Uncertain significance (Nov 22, 2023)
7-123117532-G-T		not specified	Uncertain significance (Nov 15, 2021)
7-123119112-A-G		not specified	Uncertain significance (May 01, 2022)
7-123119143-A-C		not specified	Uncertain significance (Nov 30, 2022)
7-123119167-T-C		not specified	Uncertain significance (Feb 05, 2024)
7-123119188-G-A		not specified	Uncertain significance (Aug 02, 2023)
7-123123133-C-T		not specified	Uncertain significance (Jun 06, 2023)
7-123123157-C-A		not specified	Uncertain significance (Jan 10, 2023)
7-123125586-G-A		not specified	Uncertain significance (Jan 08, 2024)
7-123125602-T-A		not specified	Uncertain significance (Dec 21, 2022)
7-123129384-T-A		not specified	Uncertain significance (Dec 01, 2022)
7-123129389-G-T		not specified	Uncertain significance (Feb 05, 2024)
7-123129431-G-A		not specified	Uncertain significance (Apr 07, 2022)
7-123129453-T-C		not specified	Uncertain significance (Feb 07, 2023)
7-123129458-C-T		not specified	Uncertain significance (Nov 17, 2023)
7-123134504-T-C		Abnormality of neuronal migration	Benign (Oct 31, 2014)
7-123134512-C-T		not specified	Likely benign (Jul 16, 2021)
7-123147170-C-G		not specified	Uncertain significance (Dec 12, 2023)
7-123147172-C-T		not specified	Uncertain significance (Nov 17, 2022)
7-123147252-G-A			Benign (Mar 29, 2018)
7-123147261-C-T		not specified	Uncertain significance (Mar 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC13A1	protein_coding	protein_coding	ENST00000194130	15	86456

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.23e-17	0.0200	125046	1	701	125748	0.00280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.503	293	318	0.921	0.0000157	3840
Missense in Polyphen		132	140.69	0.9382		1762
Synonymous	0.400	111	116	0.953	0.00000638	1196
Loss of Function	0.557	28	31.4	0.893	0.00000156	378

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00330	0.00330
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000110	0.000109
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.00441	0.00440
Middle Eastern	0.000110	0.000109
South Asian	0.00249	0.00245
Other	0.00376	0.00375

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sodium/sulfate cotransporter that mediates sulfate reabsorption in the kidney.
• 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;Selenoamino acid metabolism (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.899
• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.23

Haploinsufficiency Scores

• pHI: 0.244
• hipred: N
• hipred_score: 0.216

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0434

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc13a1
• Phenotype: reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; skeleton phenotype; renal/urinary system phenotype; limbs/digits/tail 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); growth/size/body region phenotype; homeostasis/metabolism 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 membrane
• Molecular function: citrate transmembrane transporter activity;succinate transmembrane transporter activity;sodium:sulfate symporter activity;sodium:dicarboxylate symporter activity