14-60115134-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001330177.2(PCNX4):c.1030C>T(p.Pro344Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001330177.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCNX4 | NM_001330177.2 | c.1030C>T | p.Pro344Ser | missense_variant | Exon 4 of 11 | ENST00000406854.6 | NP_001317106.1 | |
PCNX4 | NM_022495.5 | c.328C>T | p.Pro110Ser | missense_variant | Exon 3 of 10 | NP_071940.4 | ||
PCNX4 | XM_047431699.1 | c.1030C>T | p.Pro344Ser | missense_variant | Exon 4 of 11 | XP_047287655.1 | ||
PCNX4 | XM_047431700.1 | c.1030C>T | p.Pro344Ser | missense_variant | Exon 4 of 10 | XP_047287656.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 48
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.328C>T (p.P110S) alteration is located in exon 3 (coding exon 2) of the PCNX4 gene. This alteration results from a C to T substitution at nucleotide position 328, causing the proline (P) at amino acid position 110 to be replaced by a serine (S). 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