13-113181191-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001127202.4(PCID2):c.725G>A(p.Arg242His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,613,674 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001127202.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCID2 | ENST00000337344.9 | c.725G>A | p.Arg242His | missense_variant | Exon 10 of 14 | 2 | NM_001127202.4 | ENSP00000337405.4 | ||
PCID2 | ENST00000375477.5 | c.725G>A | p.Arg242His | missense_variant | Exon 10 of 15 | 1 | ENSP00000364626.1 | |||
PCID2 | ENST00000375479.6 | c.725G>A | p.Arg242His | missense_variant | Exon 10 of 15 | 2 | ENSP00000364628.2 | |||
PCID2 | ENST00000375457.2 | c.719G>A | p.Arg240His | missense_variant | Exon 10 of 14 | 1 | ENSP00000364606.2 | |||
PCID2 | ENST00000375459.5 | c.719G>A | p.Arg240His | missense_variant | Exon 10 of 15 | 2 | ENSP00000364608.1 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152162Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251422Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135898
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461512Hom.: 0 Cov.: 29 AF XY: 0.0000248 AC XY: 18AN XY: 727076
GnomAD4 genome AF: 0.000138 AC: 21AN: 152162Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.725G>A (p.R242H) alteration is located in exon 10 (coding exon 10) of the PCID2 gene. This alteration results from a G to A substitution at nucleotide position 725, causing the arginine (R) at amino acid position 242 to be replaced by a histidine (H). 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