rs587776919
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM2PM5PP3_StrongPP5
The NM_004826.4(ECEL1):c.1252C>T(p.Arg418Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000149 in 1,613,518 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 Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R418S) has been classified as Pathogenic.
Frequency
Consequence
NM_004826.4 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 |
---|---|---|---|---|---|---|---|
ECEL1 | NM_004826.4 | c.1252C>T | p.Arg418Cys | missense_variant | 7/18 | ENST00000304546.6 | |
ECEL1 | NM_001290787.2 | c.1252C>T | p.Arg418Cys | missense_variant | 7/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ECEL1 | ENST00000304546.6 | c.1252C>T | p.Arg418Cys | missense_variant | 7/18 | 1 | NM_004826.4 | P4 | |
ECEL1 | ENST00000409941.1 | c.1252C>T | p.Arg418Cys | missense_variant | 6/17 | 1 | A1 | ||
ECEL1 | ENST00000482346.1 | n.1563C>T | non_coding_transcript_exon_variant | 6/17 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250256Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135420
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461284Hom.: 0 Cov.: 33 AF XY: 0.0000193 AC XY: 14AN XY: 726958
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74378
ClinVar
Submissions by phenotype
Distal arthrogryposis type 5D Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 10, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at