NM_003002.4(SDHD):c.267_281del (p.Ala90_Ser94del) AND Hereditary Paraganglioma-Pheochromocytoma Syndromes

Clinical significance:Likely pathogenic (Last evaluated: May 14, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001194404.1

Allele description [Variation Report for NM_003002.4(SDHD):c.267_281del (p.Ala90_Ser94del)]

NM_003002.4(SDHD):c.267_281del (p.Ala90_Ser94del)

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.267_281del (p.Ala90_Ser94del)
HGVS:
  • NC_000011.10:g.112088964_112088978del
  • NG_012337.3:g.7118_7132del
  • NG_033145.1:g.2823_2837del
  • NM_001276503.2:c.169+991_169+1005del
  • NM_001276504.2:c.150_164del
  • NM_001276506.2:c.267_281del
  • NM_003002.4:c.267_281delMANE SELECT
  • NP_001263433.1:p.Ala51_Ser55del
  • NP_001263435.1:p.Ala90_Ser94del
  • NP_002993.1:p.Ala90_Ser94del
  • LRG_9t1:c.267_281del
  • LRG_9:g.7118_7132del
  • LRG_9p1:p.Ala90_Ser94del
  • NC_000011.9:g.111959688_111959702del
  • NM_003002.3:c.267_281del
  • NR_077060.2:n.302_316del
Molecular consequence:
  • NM_001276504.2:c.150_164del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001276506.2:c.267_281del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_003002.4:c.267_281del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001276503.2:c.169+991_169+1005del - intron variant - [Sequence Ontology: SO:0001627]
  • NR_077060.2:n.302_316del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Hereditary Paraganglioma-Pheochromocytoma Syndromes (PGL-PCC)
Synonyms:
Hereditary Paragangliomas and Pheochromocytomas
Identifiers:
MONDO: MONDO:0017366; MedGen: C1708353

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001363921Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Likely pathogenic
(May 14, 2019)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001363921.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: SDHD c.267_281del15 (p.Ala90_Ser94del) results in an in-frame deletion that is predicted to remove 5 amino acids from the encoded protein. The variant was absent in 251460 control chromosomes (gnomAD). To our knowledge, no occurrence of c.267_281del15 in individuals affected with Hereditary Paraganglioma-Pheochromocytoma Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Small in-frame deletions overlapping with our variant of interest have been reported in patients with Phaeochromocytoma (Met91_Ser94del) and Paraganglioma (Tyr93del and Asp92_Leu95del) (HGMD). In addition, missense variants affecting codon 92 that is found within the deleted region of our variant of interest have been reported numerous patients, suggesting that this region may be critical for protein function. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 14, 2021

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