rs532757890
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PP3_ModeratePP5
The NM_004826.4(ECEL1):c.1210C>T(p.Arg404Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,612,578 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004826.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ECEL1 | NM_004826.4 | c.1210C>T | p.Arg404Cys | missense_variant | Exon 7 of 18 | ENST00000304546.6 | NP_004817.2 | |
ECEL1 | NM_001290787.2 | c.1210C>T | p.Arg404Cys | missense_variant | Exon 7 of 18 | NP_001277716.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ECEL1 | ENST00000304546.6 | c.1210C>T | p.Arg404Cys | missense_variant | Exon 7 of 18 | 1 | NM_004826.4 | ENSP00000302051.1 | ||
ECEL1 | ENST00000409941.1 | c.1210C>T | p.Arg404Cys | missense_variant | Exon 6 of 17 | 1 | ENSP00000386333.1 | |||
ECEL1 | ENST00000482346.1 | n.1521C>T | non_coding_transcript_exon_variant | Exon 6 of 17 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248584Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134606
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1460286Hom.: 0 Cov.: 33 AF XY: 0.00000826 AC XY: 6AN XY: 726396
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152292Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74462
ClinVar
Submissions by phenotype
Distal arthrogryposis type 5D Pathogenic:3Uncertain:2
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not provided Pathogenic:2
Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 26752647, 23829171, 30131190) -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at