SLC13A2

solute carrier family 13 member 2, the group of Solute carrier family 13

Basic information

Region (hg38): 17:28473293-28497781

Links

ENSG00000007216 ∙ NCBI:9058 ∙ OMIM:604148 ∙ HGNC:10917 ∙ Uniprot:Q13183 ∙ 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 SLC13A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC13A2 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			28	2		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	2	0

Variants in SLC13A2

This is a list of pathogenic ClinVar variants found in the SLC13A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-28473725-T-C		not specified	Uncertain significance (Apr 04, 2023)
17-28473731-G-A		not specified	Uncertain significance (Mar 31, 2022)
17-28473803-G-A		not specified	Likely benign (Dec 06, 2022)
17-28489337-T-C		not specified	Uncertain significance (Aug 08, 2023)
17-28490403-G-A		not specified	Uncertain significance (Jun 19, 2024)
17-28490472-A-G		not specified	Uncertain significance (Mar 16, 2024)
17-28490517-G-A		not specified	Uncertain significance (Feb 01, 2023)
17-28490545-G-T		not specified	Uncertain significance (Jun 02, 2024)
17-28490581-G-A		not specified	Uncertain significance (Sep 26, 2022)
17-28490723-G-C		not specified	Uncertain significance (Nov 07, 2023)
17-28490742-T-C		not specified	Uncertain significance (Sep 22, 2022)
17-28490817-C-T		not specified	Uncertain significance (May 08, 2024)
17-28490851-C-A		not specified	Uncertain significance (Sep 22, 2023)
17-28490877-C-A		not specified	Uncertain significance (Jul 05, 2023)
17-28491461-C-T		not specified	Uncertain significance (Feb 15, 2023)
17-28491469-T-G		not specified	Uncertain significance (Oct 27, 2022)
17-28491752-G-A		not specified	Uncertain significance (Jul 15, 2021)
17-28491764-G-A		not specified	Uncertain significance (Oct 27, 2022)
17-28491800-A-G		not specified	Uncertain significance (Sep 16, 2021)
17-28493575-C-T		not specified	Uncertain significance (Feb 10, 2022)
17-28493585-T-C		not specified	Uncertain significance (Dec 21, 2022)
17-28493596-G-C		not specified	Uncertain significance (Jul 14, 2021)
17-28493644-G-A		not specified	Uncertain significance (Jun 16, 2023)
17-28493651-G-A		not specified	Likely benign (Aug 02, 2023)
17-28493735-C-T		not specified	Uncertain significance (Jun 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC13A2	protein_coding	protein_coding	ENST00000444914	12	24489

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.29e-13	0.165	125620	0	128	125748	0.000509

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.963	343	397	0.864	0.0000235	4166
Missense in Polyphen		131	165	0.79392		1773
Synonymous	-0.253	186	182	1.02	0.0000125	1362
Loss of Function	0.944	23	28.4	0.809	0.00000148	276

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000757	0.000753
Ashkenazi Jewish	0.000597	0.000595
East Asian	0.000708	0.000707
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000547	0.000545
Middle Eastern	0.000708	0.000707
South Asian	0.000997	0.000915
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cotransport of sodium ions and dicarboxylates such as succinate and citrate.
• 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;Butanoate metabolism;TCA cycle (Consensus)

Intolerance Scores

• loftool: 0.874
• rvis_EVS: -0.37
• rvis_percentile_EVS: 28.16

Haploinsufficiency Scores

• pHI: 0.265
• hipred: N
• hipred_score: 0.291
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.162

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc13a2
• Phenotype: homeostasis/metabolism phenotype; renal/urinary system phenotype

Gene ontology

• Biological process: sodium ion transport;dicarboxylic acid transport;transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;membrane;integral component of membrane;extracellular exosome
• Molecular function: low-affinity sodium:dicarboxylate symporter activity