SLC25A31

protein-coding

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

Gene summary

The protein encoded by this gene is a member of the ADP/ATP carrier family of proteins that exchange cytosolic ADP for matrix ATP in the mitochondria. Cells over-expressing this gene have been shown to display an anti-apoptotic phenotype. This protein is also thought to play a role in spermatogenesis, where it is believed to associate with a part of the flagellar cytoskeleton and with glycolytic enzymes. Male mice with mutations in the mouse ortholog of this gene are sterile and spermatocytes display an early meiotic arrest phenotype. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]

MANE transcript

NM_031291.4

Inheritance

—

ClinVar variants

U:36

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.9

Max pathogenic AF

—

Genomic locus

chr4:127,730,400-127,774,292

External References & Databases

Ensembl (ENSG00000151475)

Transcript & Mutation Effects

hg38 • Region Span ~43.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC25A31 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 36

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031291.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			36 clinvar			36
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	36	0	0	36

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031291.4	RefSeq	NP_112581.1	6	MANE Select
ENST00000281154.6	Ensembl	ENSP00000281154.4	6	MANE Select
NM_001318467.2	RefSeq	NP_001305396.1	7	Standard
ENST00001098262.1	Ensembl	ENSP00000768068.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

Biological Process

ADP transport
ATP transport
transmembrane transport

Molecular Function

ATP:ADP antiporter activity

Cellular Component

nucleus
mitochondrion
mitochondrial inner membrane
integral component of membrane
motile cilium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000281154
Coding exons: 6
Length: 43916
Individuals with no LoFs: 125582
Homozygous LoFs: 0
Heterozygous LoFs: 166
Defined: 125748
p: 0.000660

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.631	168	193	0.872	0.0000119	2026
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00035	0.00035	rare
Ashkenazi Jewish	0.00021	0.00020	rare
East Asian	0.00028	0.00027	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00014	0.00013	rare
South Asian	0.0041	0.0041	notable
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.126

Intolerance Scores

LoFtool: 0.584
RVIS EVS: -0.14
RVIS percentile EVS: 43.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.605

Gene Damage Prediction

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