rs587776918
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM4PP5
The NM_004826.4(ECEL1):c.344_355del(p.Asn115_Ala118del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 33)
Consequence
ECEL1
NM_004826.4 inframe_deletion
NM_004826.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.47
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 Uncertain_significance. Variant got 3 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_004826.4.
PP5
?
Variant 2-232486298-CTGGCGTCCAGGT-C is Pathogenic according to our data. Variant chr2-232486298-CTGGCGTCCAGGT-C is described in ClinVar as [Pathogenic]. Clinvar id is 39489.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr2-232486298-CTGGCGTCCAGGT-C is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ECEL1 | NM_004826.4 | c.344_355del | p.Asn115_Ala118del | inframe_deletion | 2/18 | ENST00000304546.6 | |
ECEL1 | NM_001290787.2 | c.344_355del | p.Asn115_Ala118del | inframe_deletion | 2/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ECEL1 | ENST00000304546.6 | c.344_355del | p.Asn115_Ala118del | inframe_deletion | 2/18 | 1 | NM_004826.4 | P4 | |
ECEL1 | ENST00000409941.1 | c.344_355del | p.Asn115_Ala118del | inframe_deletion | 1/17 | 1 | A1 | ||
ECEL1 | ENST00000482346.1 | n.548_559del | non_coding_transcript_exon_variant | 2/17 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
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 | literature only | OMIM | Jan 10, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at