SLC25A11

solute carrier family 25 member 11, the group of Solute carrier family 25

Basic information

Region (hg38): 17:4937130-4940053

Previous symbols: [ "SLC20A4" ]

Links

ENSG00000108528 ∙ NCBI:8402 ∙ OMIM:604165 ∙ HGNC:10981 ∙ Uniprot:Q02978 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hereditary pheochromocytoma-paraganglioma (Supportive), mode of inheritance: AD
• paragangliomas 6 (Limited), mode of inheritance: Unknown
• paragangliomas 6 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Pheochromocytoma/paraganglioma syndrome 6	AD	Oncologic	The condition can involve increased risk of the development of ceratain types of neoplasms, and awareness may allow early diagnosis and management	Oncologic	29431636

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC25A11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A11 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	3		4
missense			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	3	1	5
Total	0	0	24	7	1

Variants in SLC25A11

This is a list of pathogenic ClinVar variants found in the SLC25A11 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-4937761-G-A			Uncertain significance (Jun 19, 2024)
17-4937769-G-A			Uncertain significance (Nov 19, 2024)
17-4937791-A-C		not specified	Uncertain significance (Oct 07, 2024)
17-4937795-G-A			Uncertain significance (Sep 12, 2024)
17-4937829-T-C			Uncertain significance (Oct 02, 2024)
17-4937837-C-T			Likely benign (Oct 02, 2024)
17-4937854-G-A			Likely benign (May 29, 2024)
17-4937858-G-T		not specified • Paragangliomas 6	Uncertain significance (Jan 11, 2025)
17-4937874-C-T		not specified	Uncertain significance (Nov 19, 2024)
17-4937875-G-A		not specified	Uncertain significance (Nov 13, 2024)
17-4938039-T-G		not specified	Uncertain significance (Nov 17, 2022)
17-4938042-G-A			Uncertain significance (Dec 15, 2024)
17-4938058-T-A		not specified	Uncertain significance (Jul 27, 2024)
17-4938088-C-T			Benign (Jan 25, 2025)
17-4938094-G-T			Likely benign (Jun 24, 2024)
17-4938145-C-A			Benign (Nov 06, 2024)
17-4938155-G-T			Uncertain significance (May 01, 2024)
17-4938164-C-T		not specified	Uncertain significance (Sep 11, 2024)
17-4938176-G-T		Paragangliomas 6	Pathogenic (Oct 17, 2023)
17-4938183-G-A		Paragangliomas 6	Pathogenic (Oct 17, 2023)
17-4938220-C-T		not specified	Conflicting classifications of pathogenicity (Jan 12, 2025)
17-4938262-G-A			Uncertain significance (Jun 23, 2024)
17-4938269-C-T			Likely benign (Jul 19, 2024)
17-4938400-G-A		SLC25A11-related disorder	Likely benign (Aug 07, 2019)
17-4938405-C-T		not specified	Uncertain significance (Jun 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC25A11	protein_coding	protein_coding	ENST00000225665	8	3122

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.535	0.465	125716	0	7	125723	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.49	105	205	0.511	0.0000134	2008
Missense in Polyphen		20	72.57	0.27559		608
Synonymous	-0.516	88	82.1	1.07	0.00000516	666
Loss of Function	2.89	3	15.2	0.198	8.47e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the transport of 2-oxoglutarate across the inner mitochondrial membrane in an electroneutral exchange for malate or other dicarboxylic acids, and plays an important role in several metabolic processes, including the malate-aspartate shuttle, the oxoglutarate/isocitrate shuttle, in gluconeogenesis from lactate, and in nitrogen metabolism (By similarity). Maintains mitochondrial fusion and fission events, and the organization and morphology of cristae (PubMed:21448454). Involved in the regulation of apoptosis (By similarity). {ECO:0000250|UniProtKB:P97700, ECO:0000250|UniProtKB:Q9CR62, ECO:0000269|PubMed:21448454}.
• Pathway: Transfer of Acetyl Groups into Mitochondria;Malate-Aspartate Shuttle;Gluconeogenesis;Glycogenosis, Type IA. Von gierke disease;Glycogenosis, Type IC;Glycogen Storage Disease Type 1A (GSD1A) or Von Gierke Disease;Triosephosphate isomerase;Fructose-1,6-diphosphatase deficiency;Phosphoenolpyruvate carboxykinase deficiency 1 (PEPCK1);Glycogenosis, Type IB;Metabolism of carbohydrates;Metabolism;TCA cycle;Gluconeogenesis;Glucose metabolism (Consensus)

Recessive Scores

• pRec: 0.318

Intolerance Scores

• loftool: 0.129
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.269
• hipred: Y
• hipred_score: 0.686
• ghis: 0.616

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc25a11

Gene ontology

• Biological process: gluconeogenesis;alpha-ketoglutarate transport;transmembrane transport
• Cellular component: nucleus;mitochondrion;mitochondrial inner membrane;integral component of plasma membrane
• Molecular function: RNA binding;oxoglutarate:malate antiporter activity