chr1-172441764-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_ModeratePM2PP5_Moderate
The NM_153747.2(PIGC):c.859G>T(p.Glu287Ter) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000141 in 1,417,246 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. E287E) has been classified as Likely benign.
Frequency
Consequence
NM_153747.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGC | NM_153747.2 | c.859G>T | p.Glu287Ter | stop_gained | 2/2 | ENST00000344529.5 | |
C1orf105 | NM_139240.4 | c.22-3309C>A | intron_variant | ENST00000367727.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGC | ENST00000344529.5 | c.859G>T | p.Glu287Ter | stop_gained | 2/2 | 1 | NM_153747.2 | P1 | |
C1orf105 | ENST00000367727.9 | c.22-3309C>A | intron_variant | 1 | NM_139240.4 | P1 | |||
PIGC | ENST00000484368.1 | n.96+2224G>T | intron_variant, non_coding_transcript_variant | 1 | |||||
PIGC | ENST00000367728.1 | c.859G>T | p.Glu287Ter | stop_gained | 1/1 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000139 AC: 3AN: 215910Hom.: 0 AF XY: 0.0000259 AC XY: 3AN XY: 115654
GnomAD4 exome AF: 0.00000141 AC: 2AN: 1417246Hom.: 0 Cov.: 30 AF XY: 0.00000285 AC XY: 2AN XY: 700766
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Glycosylphosphatidylinositol biosynthesis defect 16 Pathogenic:1
Pathogenic, criteria provided, single submitter | research | Laboratory of Medical Genetics, University of Torino | Nov 29, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at