chr11-126204274-A-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_032795.3(RPUSD4):āc.851T>Cā(p.Leu284Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,613,708 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (ā ).
Frequency
Consequence
NM_032795.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPUSD4 | NM_032795.3 | c.851T>C | p.Leu284Pro | missense_variant | 6/7 | ENST00000298317.9 | |
RPUSD4 | NM_001363516.2 | c.851T>C | p.Leu284Pro | missense_variant | 6/7 | ||
RPUSD4 | NM_001144827.2 | c.758T>C | p.Leu253Pro | missense_variant | 6/7 | ||
RPUSD4 | XM_011543039.3 | c.272T>C | p.Leu91Pro | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPUSD4 | ENST00000298317.9 | c.851T>C | p.Leu284Pro | missense_variant | 6/7 | 1 | NM_032795.3 | P1 | |
RPUSD4 | ENST00000533628.5 | c.758T>C | p.Leu253Pro | missense_variant | 6/7 | 1 | |||
RPUSD4 | ENST00000526942.5 | n.872T>C | non_coding_transcript_exon_variant | 6/7 | 5 | ||||
RPUSD4 | ENST00000530903.1 | n.1025T>C | non_coding_transcript_exon_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250708Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135636
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461508Hom.: 0 Cov.: 30 AF XY: 0.0000248 AC XY: 18AN XY: 727068
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at