NM_004168.4(SDHA):c.457-1G>A AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 12, 2022
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:: RCV002651872.3

Allele description [Variation Report for NM_004168.4(SDHA):c.457-1G>A]

NM_004168.4(SDHA):c.457-1G>A

Gene:

SDHA:succinate dehydrogenase complex flavoprotein subunit A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5p15.33

Genomic location:

Preferred name:

NM_004168.4(SDHA):c.457-1G>A

HGVS:

NC_000005.10:g.225882G>A
NG_012339.1:g.12642G>A
NM_001294332.2:c.313-1G>A
NM_001330758.2:c.457-1G>A
NM_004168.4:c.457-1G>AMANE SELECT
LRG_315t1:c.457-1G>A
LRG_315:g.12642G>A
NC_000005.9:g.225997G>A

Molecular consequence:

NM_001294332.2:c.313-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001330758.2:c.457-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_004168.4:c.457-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:: Mitochondrial complex II deficiency, nuclear type 1
Synonyms:: Mitochondrial complex II deficiency; Complex 2 mitochondrial respiratory chain deficiency; Succinate CoQ reductase deficiency
Identifiers:: MONDO: MONDO:0100294; MedGen: C5700310; Orphanet: 3208; OMIM: 252011

Name:: Paragangliomas 5 (PPGL5)
Synonyms:: PHEOCHROMOCYTOMA/PARAGANGLIOMA SYNDROME 5
Identifiers:: MONDO: MONDO:0013602; MedGen: C3279992; Orphanet: 29072; OMIM: 614165

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003525626	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 12, 2022)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 26269449, 28384794, 16199547, 22974104, 24781757, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003525626

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 12, 2022)

germline

clinical testing

PubMed (6)
[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

Recommendations for somatic and germline genetic testing of single pheochromocytoma and paraganglioma based on findings from a series of 329 patients.

Currás-Freixes M, Inglada-Pérez L, Mancikova V, Montero-Conde C, Letón R, Comino-Méndez I, Apellániz-Ruiz M, Sánchez-Barroso L, Aguirre Sánchez-Covisa M, Alcázar V, Aller J, Álvarez-Escolá C, Andía-Melero VM, Azriel-Mira S, Calatayud-Gutiérrez M, Díaz JÁ, Díez-Hernández A, Lamas-Oliveira C, Marazuela M, Matias-Guiu X, Meoro-Avilés A, Patiño-García A, et al.

J Med Genet. 2015 Oct;52(10):647-56. doi: 10.1136/jmedgenet-2015-103218. Epub 2015 Aug 12.

PubMed [citation]

PMID:: 26269449

Clinical Characterization of the Pheochromocytoma and Paraganglioma Susceptibility Genes SDHA, TMEM127, MAX, and SDHAF2 for Gene-Informed Prevention.

Bausch B, Schiavi F, Ni Y, Welander J, Patocs A, Ngeow J, Wellner U, Malinoc A, Taschin E, Barbon G, Lanza V, Söderkvist P, Stenman A, Larsson C, Svahn F, Chen JL, Marquard J, Fraenkel M, Walter MA, Peczkowska M, Prejbisz A, Jarzab B, et al.

JAMA Oncol. 2017 Sep 1;3(9):1204-1212. doi: 10.1001/jamaoncol.2017.0223.

PubMed [citation]

PMID:: 28384794
PMCID:: PMC5824290

See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003525626.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Disruption of this splice site has been observed in individuals with clinical features of SDHA-related conditions (PMID: 26269449, 28384794). This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 4 of the SDHA gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in SDHA are known to be pathogenic (PMID: 22974104, 24781757).

#	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: Sep 29, 2024

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