rs121965054
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PM5PP3_Strong
The NM_000274.4(OAT):āc.1180T>Cā(p.Cys394Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C394Y) has been classified as Pathogenic.
Frequency
Consequence
NM_000274.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OAT | NM_000274.4 | c.1180T>C | p.Cys394Arg | missense_variant | 10/10 | ENST00000368845.6 | NP_000265.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OAT | ENST00000368845.6 | c.1180T>C | p.Cys394Arg | missense_variant | 10/10 | 1 | NM_000274.4 | ENSP00000357838.5 | ||
OAT | ENST00000539214.5 | c.766T>C | p.Cys256Arg | missense_variant | 9/9 | 1 | ENSP00000439042.1 | |||
OAT | ENST00000471127.1 | n.690T>C | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461760Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727178
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Ornithine aminotransferase deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 1992 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 08, 2024 | Variant summary: OAT c.1180T>C (p.Cys394Arg) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. A different variant at the same codon, c.1181G>A (p.Cys394Tyr) has been listed in association with a phenotype of Gyrate Atrophy in the HGMD and ClinVar databases, suporting the functional relevance of this codon to overall OAT function. The variant was absent in 250714 control chromosomes. c.1180T>C has been reported in the literature in at-least one individuals affected with Gyrate Atrophy (Ornithine Aminotransferase Deficiency) (example, Broday_1992 cited by Doimo_2012 and Montoli_2021). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 1737786, 23076989, 33068755). ClinVar contains an entry for this variant (Variation ID: 172). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at