rs797046130

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate

The NM_001330574.2(ZNF711):​c.1838G>T​(p.Cys613Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 22)

Consequence

ZNF711
NM_001330574.2 missense

Scores

10
6
1

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 10.0
Variant links:
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 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.883

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZNF711NM_001330574.2 linkuse as main transcriptc.1838G>T p.Cys613Phe missense_variant 11/11 ENST00000674551.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZNF711ENST00000674551.1 linkuse as main transcriptc.1838G>T p.Cys613Phe missense_variant 11/11 NM_001330574.2 P1Q9Y462-3
ZNF711ENST00000360700.4 linkuse as main transcriptc.1838G>T p.Cys613Phe missense_variant 10/101 P1Q9Y462-3
ZNF711ENST00000276123.7 linkuse as main transcriptc.1700G>T p.Cys567Phe missense_variant 10/101 Q9Y462-1
ZNF711ENST00000373165.7 linkuse as main transcriptc.1700G>T p.Cys567Phe missense_variant 9/91 Q9Y462-1

Frequencies

GnomAD3 genomes
Cov.:
22
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
22

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoApr 28, 2014- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.99
BayesDel_addAF
Pathogenic
0.35
D
BayesDel_noAF
Pathogenic
0.27
CADD
Pathogenic
27
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.59
D;D;.
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.97
.;D;D
M_CAP
Uncertain
0.28
D
MetaRNN
Pathogenic
0.88
D;D;D
MetaSVM
Pathogenic
0.89
D
MutationAssessor
Pathogenic
4.2
H;H;.
MutationTaster
Benign
1.0
D;D;D;D;D
PrimateAI
Pathogenic
0.85
D
PROVEAN
Pathogenic
-10
D;D;D
REVEL
Uncertain
0.60
Sift
Uncertain
0.0010
D;D;D
Sift4G
Pathogenic
0.0010
D;D;D
Polyphen
0.99
D;D;D
Vest4
0.85
MutPred
0.66
Gain of ubiquitination at K563 (P = 0.1215);Gain of ubiquitination at K563 (P = 0.1215);.;
MVP
0.81
MPC
1.8
ClinPred
1.0
D
GERP RS
5.2
Varity_R
0.96
gMVP
0.93

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: rs797046130; hg19: chrX-84526248; API