ClinVar Miner

Submissions for variant NM_003002.4(SDHD):c.3G>C (p.Met1Ile) (rs80338842)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000492533 SCV000581230 pathogenic Hereditary cancer-predisposing syndrome 2016-08-11 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Other acmg-defined mutation (i.e. initiation codon or gross deletion),Detected in individual satisfying established diagnostic critera for classic disease without a clear mutation,Good segregation with disease (lod 1.5-3 = 5-9 meioses)
GeneReviews RCV000020522 SCV000040979 pathologic Hereditary Paraganglioma-Pheochromocytoma Syndromes 2012-08-30 no assertion criteria provided curation Converted during submission to Pathogenic.
Invitae RCV000791414 SCV000645371 pathogenic Paraganglioma and gastric stromal sarcoma; Pheochromocytoma; Paragangliomas 1; Cowden syndrome 3 2018-09-19 criteria provided, single submitter clinical testing This sequence change affects the initiator methionine of the SDHD mRNA. An alternate in-frame methionine downstream of the initiator codon is located at codon 91, which could potentially rescue translational initiation. This variant is not present in population databases (rs80338842, ExAC no frequency). This variant has been reported in the literature in individuals and families affected with head and neck paragangliomas (HNPGLs) (PMID: 11391796, 21792967, 21945342, 12782822). In addition, different changes at the initiator codon (c.1A>G, c.2T>A, and c.2T>C) have also been observed in individuals and families with HNPGLs or non-HNPGLs, and have been shown to segregate with disease in the affected families (PMID: 15066320, 21945342, 19454582, 19351833, 17576205, 22241717). ClinVar contains an entry for this variant (Variation ID: 6906). While this variant is expected to result in an absent protein product, possible rescue of translational initiation by the downstream methionine would lead to the loss of ~60% of the SDHD protein, which contains the signal peptide domain required for entering into mitochondria (PMID: 12612654, 15066320). For these reasons, this variant has been classified as Pathogenic.
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000020522 SCV000967764 pathogenic Hereditary Paraganglioma-Pheochromocytoma Syndromes 2018-03-20 criteria provided, single submitter clinical testing The c.3G>C (p.Met1?) variant in SDHD has been identified to be a Chinese founder variant and has been reported in at least 13 Chinese individuals with hereditar y paragangliomas and/or pheochromocytomas (PGL/PCC), segregating with disease in at least 10 relatives in these families (Badenhop 2001, Lee 2003, Ma 2007, Zha 2011, Wang 2012, Zhu 2015). This variant has also been reported by other clinic al laboratories in Clinvar (Variation ID: 6906) and was absent from large popula tion studies. The p.Met1? variant alters the initiation codon of the SDHD gene a nd is predicted to lead to an untranslated transcript, resulting in an absent pr otein product. Additionally, other variants at this position, resulting in the s ame impact on the protein, have been reported in individuals with PGL/PCC (Burni chon 2009, Cascon 2009, Neumayer 2007, Piccini 2012, Riemann 2004). Heterozygous loss of function of the SDHD gene is an established disease mechanism in indivi duals with hereditary PGL/PCC. In summary, this variant meets criteria to be cla ssified as pathogenic for hereditary PGL/PCC in an autosomal dominant manner bas ed upon multiple occurrences in affected individuals, segregation studies, absen ce from the general population, and the predicted impact on protein. ACMG/AMP cr iteria applied: PS4; PVS1_Strong, PM2, PP1_Strong.
OMIM RCV000007315 SCV000027512 pathogenic Paragangliomas 1 2001-07-01 no assertion criteria provided literature only

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