ClinVar Miner

Submissions for variant NM_002775.5(HTRA1):c.660C>G (p.His220Gln)

dbSNP: rs1357930157
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology RCV001090042 SCV001237481 likely pathogenic CARASIL syndrome 2020-03-21 criteria provided, single submitter clinical testing The c.660C>G variant is not present in publicly available databases like 1000 Genomes, Exome Variant Server (EVS) and Exome Aggregation Consortium (ExAC). It is present in Genome Aggregation Database (gnomAD) and dbSNP at a very low frequency (MAF: 0.00001193), in heterozygous state. The variant is not present in our in-house exome database. The variant was not reported earlier to OMIM, ClinVar or Human Genome Mutation Database (HGMD), in any affected individuals. The variant is present in a highly conserved region and in-silico pathogenicity prediction programs like SIFT, PolyPhen-2, MutationTaster2, CADD etc. predicted this variant to be likely deleterious, however there are no documented functional studies to prove this. Since the phenotype is very specific, the variant has been classified as likely pathogenic.
Invitae RCV002554804 SCV003012335 uncertain significance not provided 2022-01-26 criteria provided, single submitter clinical testing Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 870484). This variant has not been reported in the literature in individuals affected with HTRA1-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.006%). This sequence change replaces histidine, which is basic and polar, with glutamine, which is neutral and polar, at codon 220 of the HTRA1 protein (p.His220Gln).

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