rs119477054
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP2PP3_Strong
The NM_174916.3(UBR1):c.407A>T(p.His136Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,330 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H136R) has been classified as Likely pathogenic.
Frequency
Consequence
NM_174916.3 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 |
---|---|---|---|---|---|---|---|---|
UBR1 | NM_174916.3 | c.407A>T | p.His136Leu | missense_variant | 3/47 | ENST00000290650.9 | NP_777576.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UBR1 | ENST00000290650.9 | c.407A>T | p.His136Leu | missense_variant | 3/47 | 1 | NM_174916.3 | ENSP00000290650.4 | ||
UBR1 | ENST00000546274.6 | c.407A>T | p.His136Leu | missense_variant | 3/29 | 2 | ENSP00000477932.1 | |||
UBR1 | ENST00000563239.1 | n.*54A>T | non_coding_transcript_exon_variant | 2/6 | 3 | ENSP00000456502.1 | ||||
UBR1 | ENST00000563239.1 | n.*54A>T | 3_prime_UTR_variant | 2/6 | 3 | ENSP00000456502.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251268Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135806
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461330Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727000
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at