rs1555974716
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_001330574.2(ZNF711):c.1377dup(p.Tyr460IlefsTer7) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Genomes: not found (cov: 22)
Consequence
ZNF711
NM_001330574.2 frameshift
NM_001330574.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.00
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 Likely_pathogenic. Variant got 8 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 4 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant X-85270774-G-GA is Pathogenic according to our data. Variant chrX-85270774-G-GA is described in ClinVar as [Likely_pathogenic]. Clinvar id is 495110.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF711 | NM_001330574.2 | c.1377dup | p.Tyr460IlefsTer7 | frameshift_variant | 11/11 | ENST00000674551.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF711 | ENST00000674551.1 | c.1377dup | p.Tyr460IlefsTer7 | frameshift_variant | 11/11 | NM_001330574.2 | P1 | ||
ZNF711 | ENST00000276123.7 | c.1239dup | p.Tyr414IlefsTer7 | frameshift_variant | 10/10 | 1 | |||
ZNF711 | ENST00000360700.4 | c.1377dup | p.Tyr460IlefsTer7 | frameshift_variant | 10/10 | 1 | P1 | ||
ZNF711 | ENST00000373165.7 | c.1239dup | p.Tyr414IlefsTer7 | frameshift_variant | 9/9 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD3 genomes
?
Cov.:
22
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome ? Cov.: 22
GnomAD4 genome
?
Cov.:
22
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Intellectual disability, X-linked 97 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Tehran Medical Genetics Laboratory | Sep 07, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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