20-41202114-G-C

Variant summary

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

The NM_001384317.1(ZHX3):​c.2803C>G​(p.Pro935Ala) 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. 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: not found (cov: 32)

Consequence

ZHX3
NM_001384317.1 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.98
Variant links:
Genes affected
ZHX3 (HGNC:15935): (zinc fingers and homeoboxes 3) This gene encodes a member of the zinc fingers and homeoboxes (ZHX) gene family. The encoded protein contains two C2H2-type zinc fingers and five homeodomains and forms a dimer with itself or with zinc fingers and homeoboxes family member 1. In the nucleus, the dimerized protein interacts with the A subunit of the ubiquitous transcription factor nuclear factor-Y and may function as a transcriptional repressor. [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=0.10416597).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZHX3NM_001384317.1 linkc.2803C>G p.Pro935Ala missense_variant Exon 3 of 4 ENST00000683867.1 NP_001371246.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZHX3ENST00000683867.1 linkc.2803C>G p.Pro935Ala missense_variant Exon 3 of 4 NM_001384317.1 ENSP00000506788.1 Q9H4I2-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.061
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Benign
-0.51
CADD
Benign
18
DANN
Benign
0.85
DEOGEN2
Benign
0.0057
T;T;T;T
Eigen
Benign
0.16
Eigen_PC
Uncertain
0.28
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Benign
0.77
.;.;.;T
M_CAP
Benign
0.0061
T
MetaRNN
Benign
0.10
T;T;T;T
MetaSVM
Benign
-0.95
T
MutationAssessor
Uncertain
2.3
M;M;M;M
PrimateAI
Benign
0.36
T
PROVEAN
Benign
-0.16
.;N;N;.
REVEL
Benign
0.052
Sift
Benign
0.071
.;T;T;.
Sift4G
Benign
0.70
T;T;T;T
Polyphen
0.10
B;B;B;B
Vest4
0.14
MutPred
0.12
Loss of relative solvent accessibility (P = 0.0793);Loss of relative solvent accessibility (P = 0.0793);Loss of relative solvent accessibility (P = 0.0793);Loss of relative solvent accessibility (P = 0.0793);
MVP
0.33
MPC
0.24
ClinPred
0.32
T
GERP RS
5.1
Varity_R
0.074
gMVP
0.073

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: rs764199211; hg19: chr20-39830754; API