chrX-85255483-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001330574.2(ZNF711):c.304G>A(p.Glu102Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000000911 in 1,098,176 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 23)
Exomes 𝑓: 9.1e-7 ( 0 hom. 0 hem. )
Consequence
ZNF711
NM_001330574.2 missense
NM_001330574.2 missense
Scores
1
2
13
Clinical Significance
Conservation
PhyloP100: 5.06
Genes affected
ZNF711 (HGNC:13128): (zinc finger protein 711) This gene encodes a zinc finger protein of unknown function. It bears similarity to a zinc finger protein which acts as a transcriptional activator. This gene lies in a region of the X chromosome which has been associated with cognitive disability. [provided by RefSeq, Jul 2008]
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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=0.16222614).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF711 | NM_001330574.2 | c.304G>A | p.Glu102Lys | missense_variant | 5/11 | ENST00000674551.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF711 | ENST00000674551.1 | c.304G>A | p.Glu102Lys | missense_variant | 5/11 | NM_001330574.2 | P1 | ||
ZNF711 | ENST00000360700.4 | c.304G>A | p.Glu102Lys | missense_variant | 4/10 | 1 | P1 | ||
ZNF711 | ENST00000276123.7 | c.304G>A | p.Glu102Lys | missense_variant | 5/10 | 1 | |||
ZNF711 | ENST00000373165.7 | c.304G>A | p.Glu102Lys | missense_variant | 4/9 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 genomes
?
Cov.:
23
GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183487Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67921
GnomAD3 exomes
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GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1098176Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 363538
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GnomAD4 genome ? Cov.: 23
GnomAD4 genome
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Cov.:
23
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Oct 12, 2017 | The E102K variant in the ZNF711 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The E102K variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). The E102K variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved in mammals. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret E102K as a variant of uncertain significance. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;T;.
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;L
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;B;P
Vest4
MutPred
Gain of ubiquitination at E102 (P = 0.0146);Gain of ubiquitination at E102 (P = 0.0146);Gain of ubiquitination at E102 (P = 0.0146);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
Score
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at