rs1554857529
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_033100.4(CDHR1):āc.1448A>Gā(p.Glu483Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. E483Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_033100.4 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 |
---|---|---|---|---|---|---|---|
CDHR1 | NM_033100.4 | c.1448A>G | p.Glu483Gly | missense_variant | 13/17 | ENST00000623527.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDHR1 | ENST00000623527.4 | c.1448A>G | p.Glu483Gly | missense_variant | 13/17 | 1 | NM_033100.4 | P2 | |
CDHR1 | ENST00000332904.7 | c.1448A>G | p.Glu483Gly | missense_variant | 13/17 | 1 | A2 | ||
CDHR1 | ENST00000372117.6 | c.701-520A>G | intron_variant | 2 | |||||
CDHR1 | ENST00000622973.1 | c.182A>G | p.Glu61Gly | missense_variant, NMD_transcript_variant | 2/6 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461884Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727246
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Retinal dystrophy Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | NIHR Bioresource Rare Diseases, University of Cambridge | Jan 01, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at