SLC13A5

solute carrier family 13 member 5, the group of Solute carrier family 13

Basic information

Region (hg38): 17:6684719-6713377

Links

ENSG00000141485

∙ NCBI:284111 ∙ OMIM:608305 ∙ HGNC:23089 ∙ Uniprot:Q86YT5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

pyridoxine-dependent epilepsy (Supportive), mode of inheritance: AR
amelocerebrohypohidrotic syndrome (Supportive), mode of inheritance: AR
undetermined early-onset epileptic encephalopathy (Supportive), mode of inheritance: AD
developmental and epileptic encephalopathy, 25 (Strong), mode of inheritance: AR
developmental and epileptic encephalopathy, 25 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental and epileptic encephalopathy 25, with ameliogenesis imperfecta	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	Dental; Neurologic	24995870; 26384929; 27600704; 27913086
As with other conditions involving seizures, optimal seizure control is beneficial, and awareness of genetic causes may help with medication selection

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC13A5 gene.

Developmental and epileptic encephalopathy, 25 (14 variants)
not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC13A5 gene is commonly pathogenic or not. These statistics are base on transcript: . 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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2 clinvar	175 clinvar	2 clinvar	179
missense		8 clinvar	252 clinvar	1 clinvar		261
nonsense	6 clinvar	2 clinvar	1 clinvar			9
start loss			1			1
frameshift	10 clinvar	2 clinvar	1 clinvar			13
splice donor/acceptor (+/-2bp)	2 clinvar	10 clinvar				12
Total	18	22	257	176	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC13A5	protein_coding	protein_coding	ENST00000433363	12	28855

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000506	0.998	125722	0	25	125747	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	288	348	0.828	0.0000202	3702
Missense in Polyphen		81	114.27	0.70884		1209
Synonymous	-0.155	153	151	1.02	0.00000989	1171
Loss of Function	2.83	10	25.4	0.394	0.00000117	283

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.000109	0.000109
South Asian	0.000164	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: High-affinity sodium/citrate cotransporter that mediates citrate entry into cells. The transport process is electrogenic; it is the trivalent form of citrate rather than the divalent form that is recognized as a substrate. May facilitate the utilization of circulating citrate for the generation of metabolic energy and for the synthesis of fatty acids and cholesterol. {ECO:0000269|PubMed:12445824, ECO:0000269|PubMed:26384929}.;
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;TCA cycle (Consensus)

Recessive Scores

pRec: 0.121

Intolerance Scores

loftool: 0.613
rvis_EVS: -1.4
rvis_percentile_EVS: 4.19

Haploinsufficiency Scores

pHI: 0.0907
hipred: Y
hipred_score: 0.620
ghis: 0.507

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.429

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Slc13a5
Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype;

Gene ontology

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