rs765430577
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_Strong
The NM_004826.4(ECEL1):c.1184G>T(p.Arg395Leu) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000137 in 1,461,240 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R395Q) has been classified as Pathogenic.
Frequency
Consequence
NM_004826.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ECEL1 | NM_004826.4 | c.1184G>T | p.Arg395Leu | missense_variant, splice_region_variant | 6/18 | ENST00000304546.6 | |
ECEL1 | NM_001290787.2 | c.1184G>T | p.Arg395Leu | missense_variant, splice_region_variant | 6/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ECEL1 | ENST00000304546.6 | c.1184G>T | p.Arg395Leu | missense_variant, splice_region_variant | 6/18 | 1 | NM_004826.4 | P4 | |
ECEL1 | ENST00000409941.1 | c.1184G>T | p.Arg395Leu | missense_variant, splice_region_variant | 5/17 | 1 | A1 | ||
ECEL1 | ENST00000482346.1 | n.1495G>T | splice_region_variant, non_coding_transcript_exon_variant | 5/17 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461240Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726880
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at