rs72554315
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_000531.6(OTC):c.143T>C(p.Phe48Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000918 in 1,089,036 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. F48F) has been classified as Likely benign.
Frequency
Consequence
NM_000531.6 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 |
---|---|---|---|---|---|---|---|
OTC | NM_000531.6 | c.143T>C | p.Phe48Ser | missense_variant | 2/10 | ENST00000039007.5 | |
OTC | NM_001407092.1 | c.143T>C | p.Phe48Ser | missense_variant | 4/12 | ||
OTC | XM_017029556.2 | c.143T>C | p.Phe48Ser | missense_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTC | ENST00000039007.5 | c.143T>C | p.Phe48Ser | missense_variant | 2/10 | 1 | NM_000531.6 | P1 | |
OTC | ENST00000488812.1 | n.235T>C | non_coding_transcript_exon_variant | 2/6 | 5 | ||||
OTC | ENST00000643344.1 | c.143T>C | p.Phe48Ser | missense_variant, NMD_transcript_variant | 2/11 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD4 exome AF: 9.18e-7 AC: 1AN: 1089036Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 354692
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