rs1554952193
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_022772.4(EPS8L2):c.738del(p.Val247CysfsTer6) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Consequence
EPS8L2
NM_022772.4 frameshift
NM_022772.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.57
Genes affected
EPS8L2 (HGNC:21296): (EPS8 signaling adaptor L2) This gene encodes a member of the EPS8 gene family. The encoded protein, like other members of the family, is thought to link growth factor stimulation to actin organization, generating functional redundancy in the pathways that regulate actin cytoskeletal remodeling. [provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 11-721320-GC-G is Pathogenic according to our data. Variant chr11-721320-GC-G is described in ClinVar as [Pathogenic]. Clinvar id is 433530.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPS8L2 | NM_022772.4 | c.738del | p.Val247CysfsTer6 | frameshift_variant | 9/21 | ENST00000318562.13 | |
EPS8L2 | XM_017018132.2 | c.738del | p.Val247CysfsTer6 | frameshift_variant | 10/22 | ||
EPS8L2 | XM_047427411.1 | c.738del | p.Val247CysfsTer6 | frameshift_variant | 10/22 | ||
EPS8L2 | XM_047427412.1 | c.201del | p.Val68CysfsTer6 | frameshift_variant | 4/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPS8L2 | ENST00000318562.13 | c.738del | p.Val247CysfsTer6 | frameshift_variant | 9/21 | 1 | NM_022772.4 | P1 | |
ENST00000527021.2 | n.72+5655del | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 37
GnomAD4 exome
Cov.:
37
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
Hearing loss, autosomal recessive 106 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 23, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at