SLC25A2

solute carrier family 25 member 2, the group of Solute carrier family 25

Basic information

Region (hg38): 5:141302635-141304049

Links

ENSG00000120329

∙ NCBI:83884 ∙ OMIM:608157 ∙ HGNC:22921 ∙ Uniprot:Q9BXI2 ∙ 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 SLC25A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A2 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			22 clinvar			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in SLC25A2

This is a list of pathogenic ClinVar variants found in the SLC25A2 region.

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

Position	Phenotype	Significance	ClinVar
5-141303040-C-T	not specified	Uncertain significance (Sep 17, 2021)	3163616
5-141303047-C-T	not specified	Uncertain significance (May 23, 2024)	2363653
5-141303139-A-T	not specified	Uncertain significance (Feb 22, 2025)	3797029
5-141303144-G-C	not specified	Uncertain significance (Jul 27, 2024)	3443360
5-141303151-C-T	not specified	Uncertain significance (Feb 18, 2025)	3797026
5-141303177-A-T	not specified	Uncertain significance (Dec 26, 2023)	3163615
5-141303249-T-A	not specified	Uncertain significance (Feb 26, 2025)	3797030
5-141303294-T-C	not specified	Uncertain significance (Feb 01, 2023)	2460240
5-141303354-T-C	not specified	Uncertain significance (Mar 14, 2023)	2495911
5-141303381-T-G	not specified	Uncertain significance (Mar 28, 2023)	2520150
5-141303393-T-C	not specified	Uncertain significance (Jun 05, 2023)	2508168
5-141303426-G-T	not specified	Uncertain significance (Dec 27, 2023)	3163614
5-141303430-T-G	not specified	Uncertain significance (Nov 22, 2021)	2261955
5-141303453-T-C	not specified	Uncertain significance (Sep 12, 2023)	2591269
5-141303504-G-A	not specified	Uncertain significance (Mar 07, 2025)	3797028
5-141303514-C-T	not specified	Uncertain significance (Jul 12, 2023)	2593400
5-141303516-G-A	not specified	Uncertain significance (Aug 08, 2023)	2617408
5-141303555-A-C	not specified	Uncertain significance (Feb 24, 2022)	2277926
5-141303558-T-C	not specified	Uncertain significance (Aug 01, 2023)	2615057
5-141303586-T-C	not specified	Uncertain significance (Jun 19, 2024)	3319198
5-141303587-C-G	not specified	Uncertain significance (Jun 19, 2024)	3319197
5-141303612-T-C	not specified	Uncertain significance (Jul 14, 2023)	2612070
5-141303625-G-A	not specified	Uncertain significance (Dec 02, 2024)	3443359
5-141303663-C-T	not specified	Uncertain significance (May 05, 2023)	2544653
5-141303666-G-T	not specified	Uncertain significance (Jan 26, 2022)	2273947

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A2	protein_coding	protein_coding	ENST00000239451	1	1417

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00220	0.772	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.659	150	175	0.860	0.0000104	1950
Missense in Polyphen		56	65.724	0.85204		744
Synonymous	0.602	69	75.7	0.912	0.00000556	627
Loss of Function	0.963	5	7.93	0.631	4.29e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Ornithine transport across inner mitochondrial membrane, from the cytoplasm to the matrix.;
Pathway: Lysine Degradation;Hyperlysinemia I, Familial;2-aminoadipic 2-oxoadipic aciduria;Pyridoxine dependency with seizures;Saccharopinuria/Hyperlysinemia II;Glutaric Aciduria Type I;Hyperlysinemia II or Saccharopinuria;Metabolism of polyamines;Metabolism of amino acids and derivatives;Metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Vitamin H (biotin) metabolism;Urea cycle (Consensus)

Recessive Scores

pRec: 0.146

Intolerance Scores

loftool: 0.617
rvis_EVS: 0.88
rvis_percentile_EVS: 89.02

Haploinsufficiency Scores

pHI: 0.104
hipred: N
hipred_score: 0.215
ghis: 0.403

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0578

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Slc25a2
Phenotype

Gene ontology

Biological process: urea cycle;mitochondrial L-ornithine transmembrane transport
Cellular component: mitochondrial inner membrane;integral component of membrane
Molecular function: L-ornithine transmembrane transporter activity