SLC25A5

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

Basic information

Region (hg38): X:119468421-119471396

Previous symbols: [ "ANT2" ]

Links

ENSG00000005022 ∙ NCBI:292 ∙ OMIM:300150 ∙ HGNC:10991 ∙ Uniprot:P05141 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability (Limited), mode of inheritance: XL

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC25A5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A5 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				11	3	14
missense			4		4	8
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	4	11	9

Variants in SLC25A5

This is a list of pathogenic ClinVar variants found in the SLC25A5 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-119468519-A-G		not specified	Uncertain significance (Mar 04, 2024)
X-119469687-T-C		SLC25A5-related disorder	Likely benign (Nov 05, 2019)
X-119469705-A-G		SLC25A5-related disorder	Likely benign (Mar 15, 2019)
X-119469750-T-C		SLC25A5-related disorder	Likely benign (Sep 24, 2019)
X-119469752-T-C		not specified	Uncertain significance (Jun 22, 2023)
X-119469810-T-C		SLC25A5-related disorder	Likely benign (Jan 15, 2020)
X-119469855-T-G		SLC25A5-related disorder	Likely benign (Jan 22, 2020)
X-119469867-A-G		SLC25A5-related disorder	Likely benign (Jan 22, 2020)
X-119469869-C-T		not specified	Uncertain significance (Feb 14, 2023)
X-119469881-T-G			Benign (Oct 15, 2021)
X-119469906-G-A		SLC25A5-related disorder	Benign (Sep 24, 2019)
X-119469909-T-C		SLC25A5-related disorder	Benign (Sep 24, 2019)
X-119469910-G-T		SLC25A5-related disorder	Benign (Sep 24, 2019)
X-119469918-A-T		SLC25A5-related disorder	Benign (Sep 24, 2019)
X-119469998-CT-C		Small cell lung carcinoma • Lung cancer	Pathogenic (Jun 15, 2021)
X-119469999-T-G			Likely benign (Apr 01, 2024)
X-119470038-G-A			Likely benign (Mar 01, 2023)
X-119470067-T-C		Small cell lung carcinoma • Lung cancer	Pathogenic (Jun 15, 2021)
X-119470073-A-T		not specified	Uncertain significance (May 25, 2022)
X-119470097-G-T		Small cell lung carcinoma • Lung cancer	Pathogenic (Jun 15, 2021)
X-119470140-TGCAA-T		Lung cancer	Pathogenic (Jun 15, 2021)
X-119470437-T-G		SLC25A5-related disorder	Likely benign (Oct 17, 2019)
X-119470446-C-T		SLC25A5-related disorder	Likely benign (Oct 17, 2019)
X-119470449-G-A		SLC25A5-related disorder	Likely benign (Oct 17, 2019)
X-119471038-G-T		SLC25A5-related disorder	Benign (Oct 21, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A5	protein_coding	protein_coding	ENST00000317881	4	2920

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.932	0.0678	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.65	43	127	0.338	0.0000103	1910
Missense in 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

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: 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}.
• 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);Electron Transport Chain;Disease;Vpr-mediated induction of apoptosis by mitochondrial outer membrane permeabilization;Host Interactions of HIV factors;HIV Infection;Infectious disease;Metabolism;Regulation of insulin secretion;Vitamin B9 (folate) metabolism;Integration of energy metabolism;Interactions of Vpr with host cellular proteins (Consensus)

Recessive Scores

• pRec: 0.499

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.337
• hipred: Y
• hipred_score: 0.783
• ghis: 0.643

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a5
• Phenotype: cellular phenotype

Zebrafish Information Network

• Gene name: slc25a5
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: chromosome segregation;positive regulation of cell population proliferation;adenine transport;ADP transport;ATP transport;viral process;regulation of insulin secretion;transmembrane transport;negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway;cellular response to leukemia inhibitory factor
• Cellular component: nucleus;mitochondrion;mitochondrial inner membrane;integral component of plasma membrane;membrane;mitochondrial nucleoid;myelin sheath;membrane raft;MMXD complex
• Molecular function: RNA binding;ATP:ADP antiporter activity;protein binding;adenine transmembrane transporter activity;ubiquitin protein ligase binding