SLC25A10

solute carrier family 25 member 10, the group of Solute carrier family 25

Basic information

Region (hg38): 17:81712236-81721016

Previous symbols: [ "DIC" ]

Links

ENSG00000183048 ∙ NCBI:1468 ∙ OMIM:606794 ∙ HGNC:10980 ∙ Uniprot:Q9UBX3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mitochondrial DNA depletion syndrome 19 (Moderate), mode of inheritance: AR
• mitochondrial DNA depletion syndrome 19 (Limited), mode of inheritance: Unknown
• mitochondrial disease (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mitochondrial DNA depletion syndrome 19	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	29211846

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC25A10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A10 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				4	2	6
missense			19	7	2	28
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region			1			1
non coding				1		1
Total	0	2	19	12	4

Variants in SLC25A10

This is a list of pathogenic ClinVar variants found in the SLC25A10 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-81712445-G-A		not specified	Uncertain significance (Nov 12, 2021)
17-81712452-G-A		not specified	Uncertain significance (Sep 20, 2024)
17-81712491-G-A		not specified	Uncertain significance (Jun 11, 2024)
17-81712499-C-T		not specified	Uncertain significance (Jun 26, 2024)
17-81712502-C-T		not specified	Uncertain significance (Mar 19, 2024)
17-81712503-C-A		not specified	Uncertain significance (Jun 26, 2024)
17-81712503-C-G		not specified	Uncertain significance (Dec 21, 2022)
17-81714966-C-T		not specified	Uncertain significance (Oct 12, 2021)
17-81715022-G-A		not specified	Uncertain significance (Oct 01, 2024)
17-81715025-G-A		not specified	Uncertain significance (Nov 10, 2022)
17-81715029-T-C			Likely benign (May 01, 2024)
17-81715046-G-A		not specified	Uncertain significance (Mar 20, 2023)
17-81715472-C-A			Uncertain significance (Jun 01, 2024)
17-81715482-C-T		not specified	Uncertain significance (May 05, 2023)
17-81715496-C-G		not specified	Uncertain significance (Oct 04, 2024)
17-81715496-C-T		not specified	Uncertain significance (Aug 30, 2022)
17-81715521-G-A		not specified	Uncertain significance (Mar 24, 2023)
17-81715523-G-T		not specified	Uncertain significance (Oct 03, 2024)
17-81715527-G-A		not specified	Uncertain significance (Oct 21, 2024)
17-81715533-C-T		not specified	Uncertain significance (Oct 26, 2022)
17-81715543-C-G		not specified	Uncertain significance (Sep 29, 2022)
17-81715564-C-G		not specified	Uncertain significance (Dec 12, 2023)
17-81715565-G-A		not specified	Likely benign (Mar 02, 2023)
17-81715568-A-T		Mitochondrial complex I deficiency • Mitochondrial DNA depletion syndrome 19	Likely pathogenic (Apr 01, 2021)
17-81715585-C-T			Likely benign (May 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A10	protein_coding	protein_coding	ENST00000331531	11	17639

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.86e-7	0.644	125710	0	36	125746	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.625	167	191	0.873	0.0000134	1872
Missense in Polyphen		54	66.387	0.81342		615
Synonymous	0.0434	81	81.5	0.994	0.00000618	623
Loss of Function	1.08	12	16.8	0.715	8.03e-7	193

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000249	0.000243
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000416	0.000416
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.000333	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in translocation of malonate, malate and succinate in exchange for phosphate, sulfate, sulfite or thiosulfate across mitochondrial inner membrane.
• Pathway: Proximal tubule bicarbonate reclamation - Homo sapiens (human);The oncogenic action of Succinate;The oncogenic action of Fumarate;Metabolism of carbohydrates;Sulfide oxidation to sulfate;Degradation of cysteine and homocysteine;Metabolism of amino acids and derivatives;Glycolysis and Gluconeogenesis;Purine metabolism;Metabolism;Organic anion transporters;Amino acid and oligopeptide SLC transporters;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Methionine and cysteine metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Butanoate metabolism;Gluconeogenesis;Glucose metabolism;Sulfur amino acid metabolism (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.537
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.19

Haploinsufficiency Scores

• pHI: 0.183
• hipred: N
• hipred_score: 0.239
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.742

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a10

Gene ontology

• Biological process: gluconeogenesis;ion transport;dicarboxylic acid transport;mitochondrial transport;sulfate transport;thiosulfate transport;oxaloacetate transport;phosphate ion transmembrane transport;sulfide oxidation, using sulfide:quinone oxidoreductase;succinate transmembrane transport;malate transmembrane transport;oxaloacetate(2-) transmembrane transport;sulfate transmembrane transport
• Cellular component: nucleus;nucleoplasm;mitochondrion;mitochondrial inner membrane;integral component of membrane
• Molecular function: dicarboxylic acid transmembrane transporter activity;protein binding;sulfate transmembrane transporter activity;thiosulfate transmembrane transporter activity;oxaloacetate transmembrane transporter activity;malate transmembrane transporter activity;succinate transmembrane transporter activity;antiporter activity