SLC25A31

solute carrier family 25 member 31, the group of Solute carrier family 25

Basic information

Region (hg38): 4:127730399-127774292

Links

ENSG00000151475 ∙ NCBI:83447 ∙ OMIM:610796 ∙ HGNC:25319 ∙ Uniprot:Q9H0C2 ∙ 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 SLC25A31 gene.

• Inborn genetic diseases (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A31 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in SLC25A31

This is a list of pathogenic ClinVar variants found in the SLC25A31 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-127730559-C-T		not specified	Uncertain significance (Aug 09, 2021)
4-127730649-A-G		not specified	Uncertain significance (Dec 18, 2023)
4-127730672-C-T		not specified	Uncertain significance (May 17, 2023)
4-127730751-G-A		not specified	Uncertain significance (Oct 03, 2022)
4-127730753-C-G		not specified	Uncertain significance (Oct 04, 2022)
4-127744717-A-G		not specified	Uncertain significance (Dec 07, 2021)
4-127764245-C-G		not specified	Uncertain significance (Aug 01, 2022)
4-127764248-G-T		not specified	Uncertain significance (Nov 09, 2021)
4-127764285-G-T		not specified	Uncertain significance (Jun 06, 2023)
4-127764348-G-A		not specified	Uncertain significance (Sep 07, 2022)
4-127767110-A-C		not specified	Uncertain significance (Nov 21, 2022)
4-127768780-C-T		not specified	Uncertain significance (Dec 27, 2022)
4-127768833-C-T		not specified	Uncertain significance (Mar 07, 2024)
4-127768852-C-T		not specified	Uncertain significance (Oct 12, 2021)
4-127773401-C-T		not specified	Uncertain significance (Apr 22, 2022)
4-127773552-A-G		not specified	Uncertain significance (Mar 23, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A31	protein_coding	protein_coding	ENST00000281154	6	43916

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.32e-10	0.143	125582	0	166	125748	0.000660

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.631	168	193	0.872	0.0000119	2026
Missense in Polyphen		65	79.548	0.81711		873
Synonymous	1.35	58	72.6	0.798	0.00000457	641
Loss of Function	0.373	15	16.6	0.901	0.00000106	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000663	0.000661
Ashkenazi Jewish	0.000207	0.000198
East Asian	0.000277	0.000272
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000137	0.000132
Middle Eastern	0.000277	0.000272
South Asian	0.00407	0.00406
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the exchange of cytoplasmic ADP with mitochondrial ATP across the mitochondrial inner membrane. May serve to mediate energy generating and energy consuming processes in the distal flagellum, possibly as a nucleotide shuttle between flagellar glycolysis, protein phosphorylation and mechanisms of motility. {ECO:0000269|PubMed:17137571}.
• Pathway: Huntington,s disease - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Necroptosis - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Cellular senescence - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.584
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.380
• hipred: N
• hipred_score: 0.327
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.605

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a31
• Phenotype: reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: ADP transport;ATP transport;transmembrane transport
• Cellular component: nucleus;mitochondrion;mitochondrial inner membrane;integral component of membrane;motile cilium
• Molecular function: ATP:ADP antiporter activity