SLC13A3

solute carrier family 13 member 3, the group of Solute carrier family 13

Basic information

Region (hg38): 20:46557823-46684467

Links

ENSG00000158296 ∙ NCBI:64849 ∙ OMIM:606411 ∙ HGNC:14430 ∙ Uniprot:Q8WWT9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• leukoencephalopathy, acute reversible, with increased urinary alpha-ketoglutarate (Limited), mode of inheritance: AR
• leukoencephalopathy, acute reversible, with increased urinary alpha-ketoglutarate (Limited), mode of inheritance: AR
• leukoencephalopathy, acute reversible, with increased urinary alpha-ketoglutarate (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Leukoencephalopathy, acute reversible, with increased urinary alpha-ketoglutarate	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Neurologic	30635937

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC13A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC13A3 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			5	37	10	52
missense			89	1	2	92
nonsense			3			3
start loss			1			1
frameshift			1			1
inframe indel			3			3
splice donor/acceptor (+/-2bp)						0
splice region			1	3	1	5
non coding				14	3	17
Total	0	0	102	52	15

Variants in SLC13A3

This is a list of pathogenic ClinVar variants found in the SLC13A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-46560027-G-A			Uncertain significance (Oct 26, 2022)
20-46560033-G-A			Uncertain significance (Feb 18, 2022)
20-46560035-A-T			Uncertain significance (Mar 12, 2022)
20-46560074-T-C		Leukoencephalopathy, acute reversible, with increased urinary alpha-ketoglutarate • not specified	Uncertain significance (Oct 03, 2023)
20-46560083-T-A			Uncertain significance (Jan 06, 2024)
20-46560083-T-G			Uncertain significance (Nov 01, 2022)
20-46560086-A-C			Uncertain significance (Jan 26, 2023)
20-46560094-C-T			Uncertain significance (Sep 01, 2023)
20-46560101-G-A			Uncertain significance (Apr 24, 2023)
20-46560111-C-T			Uncertain significance (Aug 21, 2022)
20-46560140-T-G			Uncertain significance (Dec 02, 2021)
20-46560172-C-G			Likely benign (Jan 05, 2023)
20-46560189-C-T		Leukoencephalopathy, acute reversible, with increased urinary alpha-ketoglutarate	Pathogenic (Nov 10, 2020)
20-46560194-C-T		Malignant tumor of prostate • Leukoencephalopathy, acute reversible, with increased urinary alpha-ketoglutarate	Uncertain significance (Mar 08, 2023)
20-46560195-G-A		not specified	Uncertain significance (Dec 07, 2023)
20-46563394-T-C			Likely benign (Mar 26, 2023)
20-46563400-AT-A			Benign (Jan 15, 2024)
20-46563408-A-G			Uncertain significance (Oct 13, 2023)
20-46563444-G-A			Likely benign (Dec 03, 2021)
20-46563475-G-A			Uncertain significance (Jan 02, 2024)
20-46563500-C-T			Uncertain significance (Dec 11, 2023)
20-46563503-C-T		not specified	Uncertain significance (Oct 03, 2022)
20-46563513-A-C			Uncertain significance (Aug 14, 2023)
20-46563526-AG-A			Uncertain significance (Jun 05, 2022)
20-46563528-G-C			Benign (Dec 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC13A3	protein_coding	protein_coding	ENST00000279027	13	118252

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.45e-7	0.984	125707	0	41	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	274	348	0.788	0.0000201	3892
Missense in Polyphen		114	162.41	0.70191		1817
Synonymous	0.569	145	154	0.942	0.00000999	1257
Loss of Function	2.21	14	26.2	0.534	0.00000142	279

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000448	0.000445
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000151	0.000149
Middle Eastern	0.000109	0.000109
South Asian	0.000164	0.000163
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: High-affinity sodium-dicarboxylate cotransporter that accepts a range of substrates with 4-5 carbon atoms. The stoichiometry is probably 3 Na(+) for 1 divalent succinate.
• 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)

Recessive Scores

• pRec: 0.173

Intolerance Scores

• loftool: 0.702
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.88

Haploinsufficiency Scores

• pHI: 0.318
• hipred: Y
• hipred_score: 0.659
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.502

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc13a3

Gene ontology

• Biological process: sodium ion transport;citrate transport;succinate transmembrane transport
• Cellular component: plasma membrane;integral component of membrane;extracellular exosome
• Molecular function: citrate transmembrane transporter activity;succinate transmembrane transporter activity;high-affinity sodium:dicarboxylate symporter activity;sodium:dicarboxylate symporter activity