NM_003562.5(SLC25A11):c.715C>A (p.Pro239Thr) AND Paragangliomas 6

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 17, 2023
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000785991.2

Allele description [Variation Report for NM_003562.5(SLC25A11):c.715C>A (p.Pro239Thr)]

NM_003562.5(SLC25A11):c.715C>A (p.Pro239Thr)

Gene:

SLC25A11:solute carrier family 25 member 11 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p13.2

Genomic location:

Preferred name:

NM_003562.5(SLC25A11):c.715C>A (p.Pro239Thr)

HGVS:

NC_000017.11:g.4938176G>T
NM_001165417.2:c.682C>A
NM_001165418.2:c.562C>A
NM_003562.5:c.715C>AMANE SELECT
NP_001158889.1:p.Pro228Thr
NP_001158890.1:p.Pro188Thr
NP_003553.2:p.Pro239Thr
NC_000017.10:g.4841471G>T

Protein change:

P188T; PRO239THR

Links:

OMIM: 604165.0001; dbSNP: rs1567650859

NCBI 1000 Genomes Browser:

rs1567650859

Molecular consequence:

NM_001165417.2:c.682C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001165418.2:c.562C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_003562.5:c.715C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Paragangliomas 6
Synonyms:: PHEOCHROMOCYTOMA/PARAGANGLIOMA SYNDROME 6
Identifiers:: MONDO: MONDO:0032767; MedGen: C5193112; OMIM: 618464

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000924621	OMIM	no assertion criteria provided	Pathogenic (Oct 17, 2023)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000924621

OMIM

no assertion criteria provided

Pathogenic
(Oct 17, 2023)

germline

literature only

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Germline Mutations in the Mitochondrial 2-Oxoglutarate/Malate Carrier SLC25A11 Gene Confer a Predisposition to Metastatic Paragangliomas.

Buffet A, Morin A, Castro-Vega LJ, Habarou F, Lussey-Lepoutre C, Letouzé E, Lefebvre H, Guilhem I, Haissaguerre M, Raingeard I, Padilla-Girola M, Tran T, Tchara L, Bertherat J, Amar L, Ottolenghi C, Burnichon N, Gimenez-Roqueplo AP, Favier J.

Cancer Res. 2018 Apr 15;78(8):1914-1922. doi: 10.1158/0008-5472.CAN-17-2463. Epub 2018 Feb 5.

PubMed [citation]

PMID:: 29431636

Details of each submission

From OMIM, SCV000924621.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a 46-year-old man (patient 1) with a nonsecreting, nonmetastatic abdominal paraganglioma (PPGL6; 618464), Buffet et al. (2018) identified a germline heterozygous c.715C-A transversion (c.715C-A, NM_003562) in the SLC25A11 gene, resulting in a pro239-to-thr (P239T) substitution at a highly conserved residue. The mutation, which was found by whole-genome sequencing, was confirmed by Sanger sequencing, and was not found in the dbSNP or ExAC databases. Tumor tissue derived from the patient showed homozygosity for the mutation. Immunohistochemical studies on the tumor tissue showed absence of the SLC25A11 protein and hypermethylation of DNA and histones compared to controls. The patient had a significant family history of cancer on the paternal side, but tissue was not available from these individuals.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 28, 2023

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