chrX-18901487-G-A
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP3PP5
The NM_000292.3(PHKA2):c.3025C>T(p.Gln1009Ter) variant causes a stop gained, splice region 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. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. Q1009Q) has been classified as Uncertain significance. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000292.3 stop_gained, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHKA2 | NM_000292.3 | c.3025C>T | p.Gln1009Ter | stop_gained, splice_region_variant | 27/33 | ENST00000379942.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHKA2 | ENST00000379942.5 | c.3025C>T | p.Gln1009Ter | stop_gained, splice_region_variant | 27/33 | 1 | NM_000292.3 | P1 | |
PHKA2 | ENST00000469645.5 | n.509C>T | splice_region_variant, non_coding_transcript_exon_variant | 5/7 | 5 | ||||
PHKA2 | ENST00000473739.5 | n.117C>T | splice_region_variant, non_coding_transcript_exon_variant | 1/6 | 3 | ||||
PHKA2 | ENST00000486231.2 | n.294C>T | splice_region_variant, non_coding_transcript_exon_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD4 exome Cov.: 22
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
Glycogen storage disease IXa1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 1995 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at