NM_003361.4:c.649T>C
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_003361.4(UMOD):āc.649T>Cā(p.Cys217Arg) 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. 12/21 in silico tools predict a damaging 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. C217G) has been classified as Pathogenic.
Frequency
Consequence
NM_003361.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UMOD | ENST00000396138.9 | c.649T>C | p.Cys217Arg | missense_variant | Exon 3 of 11 | 5 | NM_003361.4 | ENSP00000379442.5 | ||
UMOD | ENST00000396134.6 | c.748T>C | p.Cys250Arg | missense_variant | Exon 4 of 12 | 2 | ENSP00000379438.2 | |||
UMOD | ENST00000570689.5 | c.649T>C | p.Cys217Arg | missense_variant | Exon 3 of 11 | 5 | ENSP00000460548.1 | |||
UMOD | ENST00000573567.5 | c.*234T>C | downstream_gene_variant | 5 | ENSP00000460374.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1413424Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 699042
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Familial juvenile hyperuricemic nephropathy type 1 Pathogenic:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at