rs863225427
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PM5PP3_ModeratePP5
The NM_003491.4(NAA10):c.128A>C(p.Tyr43Ser) 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. Y43C) has been classified as Likely pathogenic.
Frequency
Consequence
NM_003491.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAA10 | NM_003491.4 | c.128A>C | p.Tyr43Ser | missense_variant | 3/8 | ENST00000464845.6 | |
NAA10 | NM_001256120.2 | c.128A>C | p.Tyr43Ser | missense_variant | 3/8 | ||
NAA10 | NM_001256119.2 | c.128A>C | p.Tyr43Ser | missense_variant | 3/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAA10 | ENST00000464845.6 | c.128A>C | p.Tyr43Ser | missense_variant | 3/8 | 1 | NM_003491.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD4 exome Cov.: 29
GnomAD4 genome ? Cov.: 23
ClinVar
Submissions by phenotype
Ogden syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 02, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at