9-94085353-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001253829.2(PTPDC1):c.347C>T(p.Ala116Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000867 in 1,614,052 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001253829.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPDC1 | NM_001253829.2 | c.347C>T | p.Ala116Val | missense_variant | Exon 2 of 9 | ENST00000620992.5 | NP_001240758.1 | |
PTPDC1 | NM_152422.4 | c.341C>T | p.Ala114Val | missense_variant | Exon 2 of 9 | NP_689635.3 | ||
PTPDC1 | NM_177995.3 | c.185C>T | p.Ala62Val | missense_variant | Exon 3 of 10 | NP_818931.1 | ||
PTPDC1 | NM_001253830.2 | c.185C>T | p.Ala62Val | missense_variant | Exon 3 of 10 | NP_001240759.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPDC1 | ENST00000620992.5 | c.347C>T | p.Ala116Val | missense_variant | Exon 2 of 9 | 2 | NM_001253829.2 | ENSP00000477817.1 | ||
PTPDC1 | ENST00000288976.3 | c.341C>T | p.Ala114Val | missense_variant | Exon 2 of 9 | 1 | ENSP00000288976.3 | |||
PTPDC1 | ENST00000375360.7 | c.185C>T | p.Ala62Val | missense_variant | Exon 3 of 10 | 1 | ENSP00000364509.3 | |||
PTPDC1 | ENST00000650567.1 | c.185C>T | p.Ala62Val | missense_variant | Exon 4 of 11 | ENSP00000497158.1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000795 AC: 20AN: 251492Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135920
GnomAD4 exome AF: 0.0000869 AC: 127AN: 1461886Hom.: 0 Cov.: 31 AF XY: 0.0000811 AC XY: 59AN XY: 727242
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.341C>T (p.A114V) alteration is located in exon 2 (coding exon 2) of the PTPDC1 gene. This alteration results from a C to T substitution at nucleotide position 341, causing the alanine (A) at amino acid position 114 to be replaced by a valine (V). 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