rs727502815
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PM5PP3_ModeratePP5
The NM_005360.5(MAF):c.176C>A(p.Pro59His) 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. P59L) has been classified as Pathogenic.
Frequency
Consequence
NM_005360.5 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 |
---|---|---|---|---|---|---|---|
MAF | NM_005360.5 | c.176C>A | p.Pro59His | missense_variant | 1/2 | ENST00000326043.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAF | ENST00000326043.5 | c.176C>A | p.Pro59His | missense_variant | 1/2 | 1 | NM_005360.5 | A2 | |
MAF | ENST00000569649.1 | c.176C>A | p.Pro59His | missense_variant | 1/2 | 5 | P4 | ||
MAF | ENST00000393350.1 | c.176C>A | p.Pro59His | missense_variant | 1/1 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD4 exome Cov.: 36
GnomAD4 genome ? Cov.: 30
ClinVar
Submissions by phenotype
Ayme-Gripp syndrome Pathogenic:2
Pathogenic, no assertion criteria provided | not provided | Reparto di Fisiopatologia delle Malattie Genetiche, Dipartimento di Ematologia, Oncologia; Istituto Superiore di Sanità | - | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | May 07, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at