13-113200510-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001127202.4(PCID2):c.43G>A(p.Glu15Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000206 in 1,455,202 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001127202.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCID2 | ENST00000337344.9 | c.43G>A | p.Glu15Lys | missense_variant | Exon 2 of 14 | 2 | NM_001127202.4 | ENSP00000337405.4 | ||
PCID2 | ENST00000375477.5 | c.43G>A | p.Glu15Lys | missense_variant | Exon 2 of 15 | 1 | ENSP00000364626.1 | |||
PCID2 | ENST00000375479.6 | c.43G>A | p.Glu15Lys | missense_variant | Exon 2 of 15 | 2 | ENSP00000364628.2 | |||
PCID2 | ENST00000375457.2 | c.37G>A | p.Glu13Lys | missense_variant | Exon 2 of 14 | 1 | ENSP00000364606.2 | |||
PCID2 | ENST00000375459.5 | c.37G>A | p.Glu13Lys | missense_variant | Exon 2 of 15 | 2 | ENSP00000364608.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251426Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135882
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1455202Hom.: 0 Cov.: 28 AF XY: 0.00000138 AC XY: 1AN XY: 724414
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.43G>A (p.E15K) alteration is located in exon 2 (coding exon 2) of the PCID2 gene. This alteration results from a G to A substitution at nucleotide position 43, causing the glutamic acid (E) at amino acid position 15 to be replaced by a lysine (K). 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