rs1488836686
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_019040.5(ELP4):c.92G>C(p.Arg31Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Consequence
ELP4
NM_019040.5 missense
NM_019040.5 missense
Scores
3
8
8
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.67
Genes affected
ELP4 (HGNC:1171): (elongator acetyltransferase complex subunit 4) This gene encodes a component of the six subunit elongator complex, a histone acetyltransferase complex that associates directly with RNA polymerase II during transcriptional elongation. The human gene can partially complement sensitivity phenotypes of yeast ELP4 deletion mutants. This gene has also been associated with Rolandic epilepsy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]
IMMP1L (HGNC:26317): (inner mitochondrial membrane peptidase subunit 1) The mitochondrial inner membrane peptidase (IMP) complex generates mature, active proteins in the mitochondrial intermembrane space by proteolytically removing the mitochondrial targeting presequence of nuclear-encoded proteins. IMP1 and IMP2 (IMMP2L; MIM 605977) are the catalytic subunits of the IMP complex (Burri et al., 2005 [PubMed 15814844]).[supplied by OMIM, Sep 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.39611706).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ELP4 | NM_019040.5 | c.92G>C | p.Arg31Thr | missense_variant | Exon 1 of 10 | ENST00000640961.2 | NP_061913.3 | |
| ELP4 | NM_001288726.2 | c.92G>C | p.Arg31Thr | missense_variant | Exon 1 of 12 | NP_001275655.1 | ||
| ELP4 | NM_001288725.2 | c.92G>C | p.Arg31Thr | missense_variant | Exon 1 of 11 | NP_001275654.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Benign
DEOGEN2
Benign
T;.;.;.;.;.;.;.;.;.;.;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;D;D;D;D;D;D;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;.;M;.;.;.;.;.;.;.;.;.;.
PrimateAI
Uncertain
T
PROVEAN
Uncertain
.;.;D;.;D;.;.;.;.;.;.;.;D
REVEL
Benign
Sift
Uncertain
.;.;D;.;D;.;.;.;.;.;.;.;D
Sift4G
Uncertain
.;.;D;.;D;.;.;.;.;.;.;.;D
Polyphen
D;.;.;.;.;.;.;.;.;.;.;.;D
Vest4
0.54, 0.61, 0.63
MutPred
Loss of methylation at R31 (P = 0.0285);Loss of methylation at R31 (P = 0.0285);Loss of methylation at R31 (P = 0.0285);Loss of methylation at R31 (P = 0.0285);Loss of methylation at R31 (P = 0.0285);Loss of methylation at R31 (P = 0.0285);Loss of methylation at R31 (P = 0.0285);Loss of methylation at R31 (P = 0.0285);Loss of methylation at R31 (P = 0.0285);Loss of methylation at R31 (P = 0.0285);Loss of methylation at R31 (P = 0.0285);Loss of methylation at R31 (P = 0.0285);Loss of methylation at R31 (P = 0.0285);
MVP
0.64
MPC
0.38
ClinPred
D
GERP RS
Varity_R
gMVP
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
Publications
No publications associated with this variant yet.