rs201119959
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_002641.4(PIGA):c.616A>T(p.Ile206Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I206V) has been classified as Likely benign.
Frequency
Consequence
NM_002641.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGA | NM_002641.4 | c.616A>T | p.Ile206Phe | missense_variant | 2/6 | ENST00000333590.6 | |
PIGA | NM_020473.3 | c.13+4186A>T | intron_variant | ||||
PIGA | NR_033835.1 | n.457+275A>T | intron_variant, non_coding_transcript_variant | ||||
PIGA | NR_033836.1 | n.173+559A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGA | ENST00000333590.6 | c.616A>T | p.Ile206Phe | missense_variant | 2/6 | 1 | NM_002641.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD4 exome Cov.: 28
GnomAD4 genome ? Cov.: 23
ClinVar
Submissions by phenotype
Multiple congenital anomalies-hypotonia-seizures syndrome 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 06, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at