SLC25A6

solute carrier family 25 member 6, the group of Solute carrier family 25|Pseudoautosomal region 1

Basic information

Region (hg38): Y:1386152-1392113

Previous symbols: [ "ANT3" ]

Links

ENSG00000292334 ∙ NCBI:293 ∙ OMIM:300151, 403000 ∙ HGNC:10992 ∙ Uniprot:P12236 ∙ 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 SLC25A6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A6 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				12	6	18
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	12	6

Variants in SLC25A6

This is a list of pathogenic ClinVar variants found in the SLC25A6 region.

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

Position	Type	Phenotype	Significance	ClinVar
Y-1386737-G-A			Likely benign (Dec 31, 2019)
Y-1386740-G-A			Benign (Dec 31, 2019)
Y-1387331-G-A		SLC25A6-related disorder	Likely benign (Feb 16, 2021)
Y-1387425-C-G		SLC25A6-related disorder	Benign (Feb 16, 2021)
Y-1389254-G-A			Likely benign (Jan 05, 2018)
Y-1389386-C-T			Likely benign (Nov 13, 2018)
Y-1389410-C-T			Likely benign (Dec 31, 2019)
Y-1389431-G-A		SLC25A6-related disorder	Likely benign (Feb 16, 2021)
Y-1389464-C-T			Likely benign (Nov 01, 2022)
Y-1389533-G-A			Benign (Dec 31, 2019)
Y-1389572-G-A			Benign (Dec 31, 2019)
Y-1389614-A-C			Likely benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A6	protein_coding	protein_coding	ENST00000381401	4	6573

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.139	0.844	125740	0	7	125747	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.560	184	207	0.890	0.0000155	1923
Missense in Polyphen		42	68.918	0.60942		655
Synonymous	-1.92	122	97.8	1.25	0.00000848	611
Loss of Function	2.04	3	9.95	0.302	5.16e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000184	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
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 participate in the formation of the permeability transition pore complex (PTPC) responsible for the release of mitochondrial products that triggers apoptosis. {ECO:0000269|PubMed:15033708}.
• Pathway: Influenza A - Homo sapiens (human);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;Metabolism of proteins;Influenza Virus Induced Apoptosis;Host Interactions with Influenza Factors;Influenza Infection;Infectious disease;Metabolism;Regulation of insulin secretion;Vitamin B9 (folate) metabolism;EGFR1;Mitochondrial protein import;Integration of energy metabolism;Interactions of Vpr with host cellular proteins (Consensus)

Recessive Scores

• pRec: 0.440

Intolerance Scores

• loftool: 0.263
• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.37

Haploinsufficiency Scores

• pHI: 0.487
• hipred: Y
• hipred_score: 0.603
• ghis: 0.613

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.919

Gene Damage Prediction

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

Gene ontology

• Biological process: protein targeting to mitochondrion;apoptotic process;adenine transport;ADP transport;ATP transport;active induction of host immune response by virus;regulation of insulin secretion;transmembrane transport
• Cellular component: nucleus;mitochondrion;mitochondrial inner membrane;TIM23 mitochondrial import inner membrane translocase complex;integral component of membrane
• Molecular function: ATP:ADP antiporter activity;protein binding;adenine transmembrane transporter activity