NM_003002.4(SDHD):c.288_290del (p.Ala98del) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 31, 2018
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:: RCV002533749.10

Allele description [Variation Report for NM_003002.4(SDHD):c.288_290del (p.Ala98del)]

NM_003002.4(SDHD):c.288_290del (p.Ala98del)

Gene:

SDHD:succinate dehydrogenase complex subunit D [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11q23.1

Genomic location:

Preferred name:

NM_003002.4(SDHD):c.288_290del (p.Ala98del)

HGVS:

NC_000011.10:g.112088985_112088987del
NG_012337.3:g.7139_7141del
NG_033145.1:g.2814_2816del
NM_001276503.2:c.169+1012_169+1014del
NM_001276504.2:c.171_173del
NM_001276506.2:c.288_290del
NM_003002.4:c.288_290delMANE SELECT
NP_001263433.1:p.Ala59del
NP_001263435.1:p.Ala98del
NP_002993.1:p.Ala98del
LRG_9t1:c.288_290del
LRG_9:g.7139_7141del
LRG_9p1:p.Ala98del
NC_000011.9:g.111959707_111959709del
NC_000011.9:g.111959709_111959711del
NM_003002.3:c.288_290delTGC
NR_077060.2:n.323_325del

Protein change:

A59del

Links:

dbSNP: rs1566694825

NCBI 1000 Genomes Browser:

rs1566694825

Molecular consequence:

NM_001276504.2:c.171_173del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001276506.2:c.288_290del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_003002.4:c.288_290del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001276503.2:c.169+1012_169+1014del - intron variant - [Sequence Ontology: SO:0001627]
NR_077060.2:n.323_325del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Carney-Stratakis syndrome
Synonyms:: Paraganglioma and gastric stromal sarcoma; Paraganglioma and gastrointestinal stromal tumor; Paraganglioma and GIST; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0011740; MedGen: C1847319; Orphanet: 97286; OMIM: 606864

Name:: Pheochromocytoma
Synonyms:: Chromaffinoma; Chromaffin paraganglioma; Chromaffin tumor; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008233; MedGen: C0031511; Orphanet: 29072; OMIM: 171300; Human Phenotype Ontology: HP:0002666

Name:: Paragangliomas with sensorineural hearing loss
Identifiers:: MedGen: C1868633

Name:: Cowden syndrome 3 (CWS3)
Identifiers:: MONDO: MONDO:0014045; MedGen: CN166604; Orphanet: 201

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000835690	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 31, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000835690

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 31, 2018)

germline

clinical testing

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000835690.3

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

Description

This variant has not been reported in the literature in individuals with SDHD-related disease. This variant, c.288_290delTGC, results in the deletion of 1 amino acid of the SDHD protein (p.Ala98del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency). Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acid is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Nov 10, 2024

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