5-72331308-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001284405.2(PTCD2):c.-91C>T variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.0000304 in 1,613,864 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001284405.2 5_prime_UTR_premature_start_codon_gain
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 |
---|---|---|---|---|---|---|---|---|
PTCD2 | NM_024754.5 | c.401C>T | p.Pro134Leu | missense_variant | Exon 4 of 10 | ENST00000380639.10 | NP_079030.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152042Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000111 AC: 28AN: 251484Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135916
GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461704Hom.: 0 Cov.: 30 AF XY: 0.0000330 AC XY: 24AN XY: 727152
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74432
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.401C>T (p.P134L) alteration is located in exon 4 (coding exon 4) of the PTCD2 gene. This alteration results from a C to T substitution at nucleotide position 401, causing the proline (P) at amino acid position 134 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