rs397515364
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5
The NM_007129.5(ZIC2):c.1318dup(p.Leu440ProfsTer90) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
ZIC2
NM_007129.5 frameshift
NM_007129.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.151
Genes affected
ZIC2 (HGNC:12873): (Zic family member 2) This gene encodes a member of the ZIC family of C2H2-type zinc finger proteins. This protein functions as a transcriptional repressor and may regulate tissue specific expression of dopamine receptor D1. Expansion of an alanine repeat in the C-terminus of the encoded protein and other mutations in this gene cause holoprosencephaly type 5. Holoprosencephaly is the most common structural anomaly of the human brain. A polyhistidine tract polymorphism in this gene may be associated with increased risk of neural tube defects. This gene is closely linked to a gene encoding zinc finger protein of the cerebellum 5, a related family member on chromosome 13. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 7 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 6 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 13-99985400-G-GC is Pathogenic according to our data. Variant chr13-99985400-G-GC is described in ClinVar as [Pathogenic]. Clinvar id is 6638.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZIC2 | NM_007129.5 | c.1318dup | p.Leu440ProfsTer90 | frameshift_variant | 3/3 | ENST00000376335.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZIC2 | ENST00000376335.8 | c.1318dup | p.Leu440ProfsTer90 | frameshift_variant | 3/3 | 1 | NM_007129.5 | P1 | |
ZIC2 | ENST00000468291.1 | n.292dup | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
ZIC2 | ENST00000477213.1 | n.400dup | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
ZIC2 | ENST00000490085.5 | n.364dup | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 33
GnomAD4 exome
Cov.:
33
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Holoprosencephaly 5 Pathogenic:2
Pathogenic, no assertion criteria provided | curation | GeneReviews | Aug 29, 2013 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 1998 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
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Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at