6-42925267-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138296.3(PTCRA):c.431C>T(p.Pro144Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000246 in 1,588,296 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138296.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTCRA | ENST00000304672.6 | c.431C>T | p.Pro144Leu | missense_variant | Exon 4 of 4 | 1 | NM_138296.3 | ENSP00000304447.2 | ||
PTCRA | ENST00000441198.4 | c.356C>T | p.Pro119Leu | missense_variant | Exon 5 of 5 | 1 | ENSP00000409550.1 | |||
PTCRA | ENST00000446507.5 | c.110C>T | p.Pro37Leu | missense_variant | Exon 3 of 3 | 1 | ENSP00000392288.1 | |||
PTCRA | ENST00000616441.2 | c.476C>T | p.Pro159Leu | missense_variant | Exon 4 of 4 | 2 | ENSP00000477815.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 5AN: 209602Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 115832
GnomAD4 exome AF: 0.0000230 AC: 33AN: 1436058Hom.: 0 Cov.: 32 AF XY: 0.0000168 AC XY: 12AN XY: 713792
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.431C>T (p.P144L) alteration is located in exon 4 (coding exon 4) of the PTCRA gene. This alteration results from a C to T substitution at nucleotide position 431, causing the proline (P) at amino acid position 144 to be replaced by a leucine (L). 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