ClinVar Miner

Submissions for variant NM_014646.2(LPIN2):c.2621G>T (p.Cys874Phe) (rs201160155)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000219091 SCV000279016 uncertain significance not specified 2017-04-07 criteria provided, single submitter clinical testing To our knowledge, the C874F missense change in the LPIN2 gene has neither been reported as a pathogenic variant, nor has it been reported as a benign variant. The C874F variant was observed at a frequency of 0.92%, 9/978 alleles, in individuals of South Asian ancestry, including 1.47%, 3/204 alleles, in individuals of Sri Lankan Tamil ancestry, per the 1000 Genomes Consortium (McVean et al., 2012). It is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved in mammals; however, in-silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. As the data regarding the C874F variant is limited, the clinical effect of its presence, if any, is unclear.
Illumina Clinical Services Laboratory,Illumina RCV000274408 SCV000408470 likely benign Majeed syndrome 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
CeGaT Praxis fuer Humangenetik Tuebingen RCV000658798 SCV000780593 likely benign not provided 2018-05-01 criteria provided, single submitter clinical testing
Fulgent Genetics,Fulgent Genetics RCV000274408 SCV000896694 uncertain significance Majeed syndrome 2018-10-31 criteria provided, single submitter clinical testing
Invitae RCV000274408 SCV001018602 benign Majeed syndrome 2019-12-31 criteria provided, single submitter clinical testing

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