NM_003002.4(SDHD):c.33C>A (p.Cys11Ter) AND Paragangliomas 1

Germline classification:: Pathogenic (4 submissions)
Last evaluated:: Sep 26, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV002288472.12

Allele description [Variation Report for NM_003002.4(SDHD):c.33C>A (p.Cys11Ter)]

NM_003002.4(SDHD):c.33C>A (p.Cys11Ter)

Genes:

LOC126861339:BRD4-independent group 4 enhancer GRCh37_chr11:111957035-111958234 [Gene]
SDHD:succinate dehydrogenase complex subunit D [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q23.1

Genomic location:

Preferred name:

NM_003002.4(SDHD):c.33C>A (p.Cys11Ter)

HGVS:

NC_000011.10:g.112086940C>A
NG_012337.3:g.5094C>A
NG_033145.1:g.4859G>T
NM_001276503.2:c.33C>A
NM_001276504.2:c.33C>A
NM_001276506.2:c.33C>A
NM_003002.4:c.33C>AMANE SELECT
NP_001263432.1:p.Cys11Ter
NP_001263433.1:p.Cys11Ter
NP_001263435.1:p.Cys11Ter
NP_002993.1:p.Cys11Ter
LRG_9t1:c.33C>A
LRG_9:g.5094C>A
LRG_9p1:p.Cys11Ter
NC_000011.9:g.111957664C>A
NM_003002.2:c.33C>A
NM_003002.3:c.33C>A
NR_077060.2:n.68C>A

Protein change:

C11*; CYS11TER

Links:

OMIM: 602690.0025; dbSNP: rs104894309

NCBI 1000 Genomes Browser:

rs104894309

Molecular consequence:

NR_077060.2:n.68C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001276503.2:c.33C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001276504.2:c.33C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001276506.2:c.33C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_003002.4:c.33C>A - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Name:: Paragangliomas 1
Synonyms:: Paragangliomata; Glomus tumors familial 1; Paraganglioma - glomus jugulare; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008192; MedGen: C3494181; Orphanet: 29072; OMIM: 168000

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000027522	OMIM	no assertion criteria provided	Pathogenic (May 9, 2002)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV002580586	MGZ Medical Genetics Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Dec 28, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004189826	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Aug 29, 2023)	unknown	clinical testing	Citation Link,
SCV005328379	Department of Human Genetics, Hannover Medical School	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 26, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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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
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Germ-line mutations in nonsyndromic pheochromocytoma.

Neumann HP, Bausch B, McWhinney SR, Bender BU, Gimm O, Franke G, Schipper J, Klisch J, Altehoefer C, Zerres K, Januszewicz A, Eng C, Smith WM, Munk R, Manz T, Glaesker S, Apel TW, Treier M, Reineke M, Walz MK, Hoang-Vu C, Brauckhoff M, et al.

N Engl J Med. 2002 May 9;346(19):1459-66.

PubMed [citation]

PMID:: 12000816

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From OMIM, SCV000027522.5

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

Description

In the germlines of 4 unrelated patients with sporadic pheochromocytoma (PPGL1; 168000) Neumann et al. (2002) identified a heterozygous c.33C-A transversion in exon 1 of the SDHD gene, resulting in a cys11-to-ter (C11X) substitution. The mutation was not identified in 600 control chromosomes.

#	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

From MGZ Medical Genetics Center, SCV002580586.1

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

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

From Myriad Genetics, Inc., SCV004189826.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.

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

From Department of Human Genetics, Hannover Medical School, SCV005328379.1

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

Description

ACMG: PVS1, PM2_Supporting, PP4

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

Last Updated: Nov 24, 2024

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