2-232480167-A-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_004826.4(ECEL1):āc.2314T>Cā(p.Cys772Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000658 in 151,892 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 Uncertain significance (ā ).
Frequency
Consequence
NM_004826.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ECEL1 | NM_004826.4 | c.2314T>C | p.Cys772Arg | missense_variant | Exon 18 of 18 | ENST00000304546.6 | NP_004817.2 | |
ECEL1 | NM_001290787.2 | c.2308T>C | p.Cys770Arg | missense_variant | Exon 18 of 18 | NP_001277716.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ECEL1 | ENST00000304546.6 | c.2314T>C | p.Cys772Arg | missense_variant | Exon 18 of 18 | 1 | NM_004826.4 | ENSP00000302051.1 | ||
ECEL1 | ENST00000409941.1 | c.2308T>C | p.Cys770Arg | missense_variant | Exon 17 of 17 | 1 | ENSP00000386333.1 | |||
ECEL1 | ENST00000411860.5 | c.493T>C | p.Cys165Arg | missense_variant | Exon 6 of 6 | 3 | ENSP00000412683.1 | |||
ECEL1 | ENST00000482346.1 | n.2625T>C | non_coding_transcript_exon_variant | Exon 17 of 17 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151774Hom.: 0 Cov.: 33
GnomAD4 exome Cov.: 32
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151892Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74260
ClinVar
Submissions by phenotype
Distal arthrogryposis type 5D Uncertain:1
The homozygous p.Cys772Arg variant in ECEL1 was identified by our study in 1 individual with Duane retraction syndrome, congenital ptosis, and arthrogryposis, via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Engle lab (https://kirbyneuro.org/EngleLab/). The p.Cys772Arg variant in ECEL1 has not been previously reported in the literature in individuals with distal arthrogryposis type 5D. This variant is absent from large population studies. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, the clinical significance of the p.Cys772Arg variant is uncertain. ACMG/AMP Criteria applied: PP3, PM2_supporting, PM3_supporting (Richards 2015). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.