rs121434430
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 5P and 1B. PM1PM2PP5BP4
The NM_001081.4(CUBN):c.3890C>T(p.Pro1297Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000162 in 1,613,404 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1297S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001081.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CUBN | NM_001081.4 | c.3890C>T | p.Pro1297Leu | missense_variant | 27/67 | ENST00000377833.10 | |
CUBN | XM_011519708.3 | c.3890C>T | p.Pro1297Leu | missense_variant | 27/55 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CUBN | ENST00000377833.10 | c.3890C>T | p.Pro1297Leu | missense_variant | 27/67 | 1 | NM_001081.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000243 AC: 37AN: 151964Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000330 AC: 83AN: 251280Hom.: 0 AF XY: 0.000324 AC XY: 44AN XY: 135810
GnomAD4 exome AF: 0.000153 AC: 224AN: 1461440Hom.: 0 Cov.: 31 AF XY: 0.000144 AC XY: 105AN XY: 727036
GnomAD4 genome ? AF: 0.000243 AC: 37AN: 151964Hom.: 0 Cov.: 32 AF XY: 0.000350 AC XY: 26AN XY: 74196
ClinVar
Submissions by phenotype
Imerslund-Grasbeck syndrome type 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 15, 2000 | - - |
Imerslund-Grasbeck syndrome Pathogenic:1
Likely pathogenic, no assertion criteria provided | literature only | Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at