chr19-43578676-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001193621.3(PINLYP):c.157T>C(p.Cys53Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000723 in 1,383,530 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C53S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001193621.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PINLYP | NM_001193621.3 | c.157T>C | p.Cys53Arg | missense_variant | 3/6 | ENST00000599207.6 | |
PINLYP | XM_047438830.1 | c.229T>C | p.Cys77Arg | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PINLYP | ENST00000599207.6 | c.157T>C | p.Cys53Arg | missense_variant | 3/6 | 5 | NM_001193621.3 | P2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000743 AC: 1AN: 134588Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 73310
GnomAD4 exome AF: 7.23e-7 AC: 1AN: 1383530Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 682726
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 21, 2023 | The c.229T>C (p.C77R) alteration is located in exon 3 (coding exon 2) of the PINLYP gene. This alteration results from a T to C substitution at nucleotide position 229, causing the cysteine (C) at amino acid position 77 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at