rs201513124

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_019040.5(ELP4):​c.127G>A​(p.Gly43Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,930 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

ELP4
NM_019040.5 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.18423155).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ELP4NM_019040.5 linkc.127G>A p.Gly43Ser missense_variant Exon 1 of 10 ENST00000640961.2 NP_061913.3 Q96EB1-1
ELP4NM_001288726.2 linkc.127G>A p.Gly43Ser missense_variant Exon 1 of 12 NP_001275655.1 Q96EB1G5E9D4
ELP4NM_001288725.2 linkc.127G>A p.Gly43Ser missense_variant Exon 1 of 11 NP_001275654.1 Q96EB1-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ELP4ENST00000640961.2 linkc.127G>A p.Gly43Ser missense_variant Exon 1 of 10 1 NM_019040.5 ENSP00000492152.1 Q96EB1-1

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152200
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461730
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
727164
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152200
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.079
BayesDel_addAF
Benign
-0.15
T
BayesDel_noAF
Benign
-0.45
CADD
Benign
16
DANN
Uncertain
1.0
DEOGEN2
Benign
0.0077
T;.;.;.;.;.;.;.;.;.;.;.;.
Eigen
Benign
-0.19
Eigen_PC
Benign
-0.16
FATHMM_MKL
Benign
0.67
D
LIST_S2
Benign
0.79
T;T;T;T;T;T;T;T;T;T;T;T;T
M_CAP
Benign
0.039
D
MetaRNN
Benign
0.18
T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.99
T
MutationAssessor
Uncertain
2.1
M;.;M;.;.;.;.;.;.;.;.;.;.
PrimateAI
Benign
0.41
T
PROVEAN
Benign
-0.65
.;.;N;.;N;.;.;.;.;.;.;.;N
REVEL
Benign
0.055
Sift
Benign
0.14
.;.;T;.;T;.;.;.;.;.;.;.;T
Sift4G
Benign
0.44
.;.;T;.;T;.;.;.;.;.;.;.;T
Polyphen
0.73
P;.;.;.;.;.;.;.;.;.;.;.;D
Vest4
0.17, 0.18, 0.19
MutPred
0.37
Loss of catalytic residue at G43 (P = 9e-04);Loss of catalytic residue at G43 (P = 9e-04);Loss of catalytic residue at G43 (P = 9e-04);Loss of catalytic residue at G43 (P = 9e-04);Loss of catalytic residue at G43 (P = 9e-04);Loss of catalytic residue at G43 (P = 9e-04);Loss of catalytic residue at G43 (P = 9e-04);Loss of catalytic residue at G43 (P = 9e-04);Loss of catalytic residue at G43 (P = 9e-04);Loss of catalytic residue at G43 (P = 9e-04);Loss of catalytic residue at G43 (P = 9e-04);Loss of catalytic residue at G43 (P = 9e-04);Loss of catalytic residue at G43 (P = 9e-04);
MVP
0.48
MPC
0.053
ClinPred
0.86
D
GERP RS
3.6
Varity_R
0.044
gMVP
0.38

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs201513124; hg19: chr11-31531458; API