NM_017841.4(SDHAF2):c.267del (p.Phe89fs) AND Hereditary pheochromocytoma-paraganglioma

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 18, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001993114.3

Allele description [Variation Report for NM_017841.4(SDHAF2):c.267del (p.Phe89fs)]

NM_017841.4(SDHAF2):c.267del (p.Phe89fs)

Gene:

SDHAF2:succinate dehydrogenase complex assembly factor 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11q12.2

Genomic location:

Preferred name:

NM_017841.4(SDHAF2):c.267del (p.Phe89fs)

HGVS:

NC_000011.10:g.61438010del
NG_023393.1:g.12886del
NM_017841.4:c.267delMANE SELECT
NP_060311.1:p.Phe89fs
LRG_519t1:c.267del
LRG_519:g.12886del
NC_000011.9:g.61205478del
NC_000011.9:g.61205482del
NM_017841.2:c.267delT

Protein change:

F89fs

Links:

dbSNP: rs766035180

NCBI 1000 Genomes Browser:

rs766035180

Molecular consequence:

NM_017841.4:c.267del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Hereditary pheochromocytoma-paraganglioma
Synonyms:: Hereditary Paraganglioma-Pheochromocytoma Syndromes; Hereditary Paragangliomas and Pheochromocytomas
Identifiers:: MONDO: MONDO:0017366; MedGen: C1708353

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002236387	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 18, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 22241717, 26096992, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002236387

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 18, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Head and neck paragangliomas: genetic spectrum and clinical variability in 79 consecutive patients.

Piccini V, Rapizzi E, Bacca A, Di Trapani G, Pulli R, Giachè V, Zampetti B, Lucci-Cordisco E, Canu L, Corsini E, Faggiano A, Deiana L, Carrara D, Tantardini V, Mariotti S, Ambrosio MR, Zatelli MC, Parenti G, Colao A, Pratesi C, Bernini G, Ercolino T, et al.

Endocr Relat Cancer. 2012 Apr 10;19(2):149-55. doi: 10.1530/ERC-11-0369. Print 2012 Apr.

PubMed [citation]

PMID:: 22241717

Germline mutations and genotype-phenotype associations in head and neck paraganglioma patients with negative family history in China.

Zhu WD, Wang ZY, Chai YC, Wang XW, Chen DY, Wu H.

Eur J Med Genet. 2015 Sep;58(9):433-8. doi: 10.1016/j.ejmg.2015.05.008. Epub 2015 Jun 19.

PubMed [citation]

PMID:: 26096992

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002236387.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1451128). This variant has not been reported in the literature in individuals affected with SDHAF2-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change creates a premature translational stop signal (p.Phe89Leufs*9) in the SDHAF2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SDHAF2 are known to be pathogenic (PMID: 22241717, 26096992).

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

Last Updated: May 1, 2024

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