ClinVar Miner

Submissions for variant NM_000102.4(CYP17A1):c.157TTC[1] (p.Phe54del)

dbSNP: rs121434319
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001382543 SCV001581378 pathogenic not provided 2023-10-18 criteria provided, single submitter clinical testing This variant, c.160_162del, results in the deletion of 1 amino acid(s) of the CYP17A1 protein (p.Phe54del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs762179268, gnomAD 0.02%). This variant has been observed in individuals with 17 alpha-hydroxylase deficiency (PMID: 2808364, 10720067, 10877510, 19793597, 29068264). This variant is also known as p.Phe53del. ClinVar contains an entry for this variant (Variation ID: 1778). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects CYP17A1 function (PMID: 2808364, 10720067). For these reasons, this variant has been classified as Pathogenic.
Genetic Services Laboratory, University of Chicago RCV001382543 SCV002069275 pathogenic not provided 2019-02-13 criteria provided, single submitter clinical testing DNA sequence analysis of the CYP17A1 gene demonstrated a homozygous 3 base pair deletion in exon 1, c.160_162del. This sequence change results in an in-frame deletion of a single amino acid , phenylalanine, at position 54, p.Phe54del. This deletion has been previously described in three 46, XX phenotypic females with no sexual abnormalities and regular or irregular menstruation and one 46, XY phenotypic male with hypospadias and cryptorchidism (PMID: 8855840). Functional studies of the p.Phe54del in cell expression systems demonstrated a significant reduction in enzyme activity (PMID: 2808364). These collective evidences indicate that this sequence change is pathogenic.
Neuberg Centre For Genomic Medicine, NCGM RCV001826402 SCV004048132 likely pathogenic Deficiency of steroid 17-alpha-monooxygenase criteria provided, single submitter clinical testing This variant, c.160_162del, results in the deletion of 1 amino acid(s) of the CYP17A1 protein (p.Phe54del), but otherwise preserves the integrity of the reading frame. . This variant has been observed in individual(s) with 17 alpha-hydroxylase deficiency (Yanase T et al & Biason-Lauber A et al). This variant is also known as p.Phe53del in the literature. This variant has been reported to affect CYP17A1 protein function (Yanase T et al & Biason-Lauber A et al). This variant is reported with the allele frequency (0.002386%) in the gnomad and novel in 1000 genome database. It has been submitted to ClinVar as Pathogenic. This p.Phe54del causes deletion of amino acid Phenylalanine at position 54. For these reasons, this variant has been classified as Likely Pathogenic.
Baylor Genetics RCV001826402 SCV004215386 pathogenic Deficiency of steroid 17-alpha-monooxygenase 2024-03-12 criteria provided, single submitter clinical testing
OMIM RCV000001850 SCV000022006 pathogenic 17-alpha-hydroxylase/17,20-lyase deficiency, combined partial 1996-10-01 no assertion criteria provided literature only
Natera, Inc. RCV001826402 SCV002094384 pathogenic Deficiency of steroid 17-alpha-monooxygenase 2020-06-05 no assertion criteria provided clinical testing

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