rs398123038
Variant summary
Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PVS1PM2PP3_ModeratePP5
The NM_015352.2(POFUT1):c.430G>T(p.Glu144Ter) 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. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_015352.2 stop_gained, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POFUT1 | NM_015352.2 | c.430G>T | p.Glu144Ter | stop_gained, splice_region_variant | 4/7 | ENST00000375749.8 | |
POFUT1 | NM_172236.2 | c.430G>T | p.Glu144Ter | stop_gained, splice_region_variant | 4/5 | ||
POFUT1 | XM_047440079.1 | c.106G>T | p.Glu36Ter | stop_gained, splice_region_variant | 3/6 | ||
POFUT1 | XR_007067447.1 | n.492G>T | splice_region_variant, non_coding_transcript_exon_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POFUT1 | ENST00000375749.8 | c.430G>T | p.Glu144Ter | stop_gained, splice_region_variant | 4/7 | 1 | NM_015352.2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 29
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Dowling-Degos disease 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 06, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at