ClinVar Miner

Submissions for variant NM_001083116.3(PRF1):c.836G>A (p.Cys279Tyr)

gnomAD frequency: 0.00002  dbSNP: rs104894182
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV003466860 SCV004206476 likely pathogenic Aplastic anemia 2023-07-06 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000014714 SCV004294731 pathogenic Familial hemophagocytic lymphohistiocytosis 2 2023-09-08 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects PRF1 function (PMID: 15755897). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on PRF1 protein function. ClinVar contains an entry for this variant (Variation ID: 13714). This missense change has been observed in individual(s) with hemophagocytic lymphohistiocytosis (PMID: 10583959, 12060139, 17627755; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (rs104894182, gnomAD 0.004%). This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 279 of the PRF1 protein (p.Cys279Tyr).
OMIM RCV000014714 SCV000034969 pathogenic Familial hemophagocytic lymphohistiocytosis 2 1999-12-03 no assertion criteria provided literature only

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