SLC25A40

solute carrier family 25 member 40, the group of Solute carrier family 25

Basic information

Region (hg38): 7:87833568-87876360

Links

ENSG00000075303 ∙ NCBI:55972 ∙ OMIM:610821 ∙ HGNC:29680 ∙ Uniprot:Q8TBP6 ∙ 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 SLC25A40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A40 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				1		1
missense			17	4		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	5	0

Variants in SLC25A40

This is a list of pathogenic ClinVar variants found in the SLC25A40 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-87836293-T-G		not specified	Uncertain significance (Dec 20, 2023)
7-87836331-G-A		not specified	Uncertain significance (Dec 05, 2024)
7-87836775-T-C		not specified	Uncertain significance (Jan 23, 2024)
7-87836795-T-C		not specified	Uncertain significance (Oct 12, 2022)
7-87836805-T-C		SLC25A40-related disorder	Likely benign (Aug 27, 2019)
7-87841646-A-G		SLC25A40-related disorder	Likely benign (Sep 18, 2019)
7-87841651-T-C		not specified	Uncertain significance (Jun 29, 2023)
7-87841699-T-C		not specified	Uncertain significance (Feb 22, 2023)
7-87841708-C-A		not specified	Uncertain significance (Dec 21, 2023)
7-87843780-A-T		not specified	Uncertain significance (Dec 01, 2022)
7-87843822-A-T		not specified	Uncertain significance (Dec 03, 2021)
7-87843830-T-G		not specified	Uncertain significance (Jan 09, 2024)
7-87843841-T-G		not specified	Uncertain significance (Jun 06, 2023)
7-87843851-T-A		not specified	Uncertain significance (Dec 06, 2024)
7-87847036-A-T		not specified	Uncertain significance (Nov 01, 2021)
7-87847044-A-G		not specified	Uncertain significance (Aug 04, 2023)
7-87847051-C-T		not specified	Likely benign (May 23, 2023)
7-87847075-T-C		not specified	Uncertain significance (Mar 17, 2023)
7-87847942-G-A		SLC25A40-related disorder	Likely benign (Dec 01, 2022)
7-87849899-C-T		SLC25A40-related disorder	Likely benign (Mar 31, 2022)
7-87854214-T-C		not specified	Uncertain significance (Dec 17, 2021)
7-87854253-C-G		not specified	Uncertain significance (Dec 22, 2023)
7-87854256-T-G		not specified	Uncertain significance (Feb 12, 2024)
7-87854289-T-C		not specified	Uncertain significance (Sep 13, 2023)
7-87858652-C-T		not specified	Uncertain significance (May 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A40	protein_coding	protein_coding	ENST00000341119	10	42790

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.93e-7	0.822	125669	0	73	125742	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.906	132	165	0.801	0.00000751	2185
Missense in Polyphen		51	68.685	0.74252		940
Synonymous	-0.0977	55	54.1	1.02	0.00000249	619
Loss of Function	1.44	13	20.0	0.651	9.71e-7	252

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00155	0.00152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000230	0.000229
Middle Eastern	0.000272	0.000272
South Asian	0.000200	0.000196
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.694
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.282
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.403

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a40
• Phenotype: normal phenotype

Gene ontology

• Biological process: transmembrane transport
• Cellular component: mitochondrial inner membrane;integral component of membrane
• Molecular function: transmembrane transporter activity