chrX-38408752-C-G
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PS1_ModeratePM2PM5PP3_StrongPP5
The NM_000531.6(OTC):c.674C>G(p.Pro225Arg) variant causes a missense change. 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 nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P225T) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000531.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OTC | NM_000531.6 | c.674C>G | p.Pro225Arg | missense_variant | 7/10 | ENST00000039007.5 | NP_000522.3 | |
OTC | NM_001407092.1 | c.674C>G | p.Pro225Arg | missense_variant | 9/12 | NP_001394021.1 | ||
OTC | XM_017029556.2 | c.674C>G | p.Pro225Arg | missense_variant | 7/9 | XP_016885045.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OTC | ENST00000039007.5 | c.674C>G | p.Pro225Arg | missense_variant | 7/10 | 1 | NM_000531.6 | ENSP00000039007 | P1 | |
OTC | ENST00000643344.1 | c.*424C>G | 3_prime_UTR_variant, NMD_transcript_variant | 8/11 | ENSP00000496606 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Cov.: 28
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | GenMed Metabolism Lab | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at