rs878853118
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PVS1PP5
The NM_004826.4(ECEL1):c.797_801delinsGCT(p.Asp266GlyfsTer15) variant causes a frameshift change. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 34)
Consequence
ECEL1
NM_004826.4 frameshift
NM_004826.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.06
Genes affected
ECEL1 (HGNC:3147): (endothelin converting enzyme like 1) This gene encodes a member of the M13 family of endopeptidases. Members of this family are zinc-containing type II integral-membrane proteins that are important regulators of neuropeptide and peptide hormone activity. Mutations in this gene are associated with autosomal recessive distal arthrogryposis, type 5D. This gene has multiple pseudogenes on chromosome 2. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PP5
?
Variant 2-232485253-CCCAT-AGC is Pathogenic according to our data. Variant chr2-232485253-CCCAT-AGC is described in ClinVar as [Pathogenic]. Clinvar id is 242402.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ECEL1 | NM_004826.4 | c.797_801delinsGCT | p.Asp266GlyfsTer15 | frameshift_variant | 3/18 | ENST00000304546.6 | |
ECEL1 | NM_001290787.2 | c.797_801delinsGCT | p.Asp266GlyfsTer15 | frameshift_variant | 3/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ECEL1 | ENST00000304546.6 | c.797_801delinsGCT | p.Asp266GlyfsTer15 | frameshift_variant | 3/18 | 1 | NM_004826.4 | P4 | |
ECEL1 | ENST00000409941.1 | c.797_801delinsGCT | p.Asp266GlyfsTer15 | frameshift_variant | 2/17 | 1 | A1 | ||
ECEL1 | ENST00000482346.1 | n.1001_1005delinsGCT | non_coding_transcript_exon_variant | 3/17 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD3 genomes
?
Cov.:
34
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 34
GnomAD4 genome
?
Cov.:
34
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Distal arthrogryposis type 5D Pathogenic:1
Pathogenic, no assertion criteria provided | research | University of Washington Center for Mendelian Genomics, University of Washington | Jan 08, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at