NM_003002.4(SDHD):c.18_21del (p.Leu7fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 23, 2020
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:: RCV002235529.14

Allele description [Variation Report for NM_003002.4(SDHD):c.18_21del (p.Leu7fs)]

NM_003002.4(SDHD):c.18_21del (p.Leu7fs)

Genes:

LOC126861339:BRD4-independent group 4 enhancer GRCh37_chr11:111957035-111958234 [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.18_21del (p.Leu7fs)

HGVS:

NC_000011.10:g.112086925_112086928del
NG_012337.3:g.5079_5082del
NG_033145.1:g.4872_4875del
NM_001276503.2:c.18_21del
NM_001276504.2:c.18_21del
NM_001276506.2:c.18_21del
NM_003002.4:c.18_21delMANE SELECT
NP_001263432.1:p.Leu7fs
NP_001263433.1:p.Leu7fs
NP_001263435.1:p.Leu7fs
NP_002993.1:p.Leu7fs
LRG_9t1:c.18_21del
LRG_9:g.5079_5082del
LRG_9p1:p.Leu7fs
NC_000011.9:g.111957648_111957651del
NC_000011.9:g.111957649_111957652del
NM_003002.3:c.18_21delGCTG
NR_077060.2:n.53_56del

Protein change:

L7fs

Links:

dbSNP: rs1555186662

NCBI 1000 Genomes Browser:

rs1555186662

Molecular consequence:

NM_001276503.2:c.18_21del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276504.2:c.18_21del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276506.2:c.18_21del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003002.4:c.18_21del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_077060.2:n.53_56del - 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
SCV001581617	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 23, 2020)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 19454582, 19802898, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001581617

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 23, 2020)

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

Nothing to display

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001581617.5

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

Description

This sequence change creates a premature translational stop signal (p.Leu7Valfs*7) in the SDHD gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in SDHD are known to be pathogenic (PMID: 19454582, 19802898). This variant has not been reported in the literature in individuals with SDHD-related conditions. ClinVar contains an entry for this variant (Variation ID: 547769).

#	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 18, 2024

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