SLC25A5

protein-coding

solute carrier family 25 member 5, the group of Solute carrier family 25

Gene summary

This gene is a member of the mitochondrial carrier subfamily of solute carrier protein genes. The product of this gene functions as a gated pore that translocates ADP from the cytoplasm into the mitochondrial matrix and ATP from the mitochondrial matrix into the cytoplasm. The protein forms a homodimer embedded in the inner mitochondria membrane. Suppressed expression of this gene has been shown to induce apoptosis and inhibit tumor growth. The human genome contains several non-transcribed pseudogenes of this gene.[provided by RefSeq, Jun 2013]

Previous symbols:

ANT2

MANE transcript

NM_001152.5

Inheritance

ClinVar variants

U:44B:13

Top phenotype

SLC25A5-related disorder

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:119,468,422-119,471,396

External References & Databases

Ensembl (ENSG00000005022)

Transcript & Mutation Effects

hg38 • Region Span ~3.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

intellectual disabilityLIMITED

Inheritance Pattern: XL

Disease ID:MONDO:0001071

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC25A5 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 11

SLC25A5-related disorderTotal: 9

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001152.5. 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			5 clinvar	7 clinvar	3 clinvar	15
missense			25 clinvar	1 clinvar	2 clinvar	28
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			13 clinvar			13
Total	0	0	44	8	5	57

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001152.5	RefSeq	NP_001143.2	4	MANE Select
ENST00000317881.9	Ensembl	ENSP00000360671.4	4	MANE Select
ENST00000879015.1	Ensembl	ENSP00000549074.1	4	Standard
ENST00000879015.2	Ensembl	ENSP00000549074.1	4	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
slc25a5	Danio rerio	Structure: head Quality: decreased size abnormal

Gene / Model

Organism

Observed Phenotype

slc25a5

Danio rerio

Structure: head

Quality: decreased size

abnormal

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

chromosome segregation
positive regulation of cell population proliferation
adenine transport
ADP transport
ATP transport

Molecular Function

RNA binding
ATP:ADP antiporter activity
protein binding
adenine transmembrane transporter activity
ubiquitin protein ligase binding

Cellular Component

nucleus
mitochondrion
mitochondrial inner membrane
integral component of plasma membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000317881
Coding exons: 4
Length: 2920
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.65	43	127	0.338	0.0000103	1910
Missense (PolyPhen)		0	22.922	0		484
Synonymous	1.14	38	48.1	0.790	0.00000378	597
Loss of Function	2.71	0	8.56	0.00	6.89e-7	126

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
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. As part of the mitotic spindle-associated MMXD complex it may play a role in chromosome segregation. {ECO:0000269|PubMed:20797633}.;

Recessive Scores

pRec: 0.499

Intolerance Scores

RVIS EVS: -0.03
RVIS percentile EVS: 51.04

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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