rs121965054
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_000274.4(OAT):c.1180T>C(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 Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C394Y) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000274.4 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 | UniProt |
---|---|---|---|---|---|---|---|
OAT | NM_000274.4 | c.1180T>C | p.Cys394Arg | missense_variant | 10/10 | ENST00000368845.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OAT | ENST00000368845.6 | c.1180T>C | p.Cys394Arg | missense_variant | 10/10 | 1 | NM_000274.4 | P1 | |
OAT | ENST00000539214.5 | c.766T>C | p.Cys256Arg | missense_variant | 9/9 | 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 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at