rs398124241
chr13-99982753-CCCACCACCACCACCA-Cchr13-99982753-CCCACCACCACCACCA-CCCAchr13-99982753-CCCACCACCACCACCA-CCCACCAchr13-99982753-CCCACCACCACCACCA-CCCACCACCAchr13-99982753-CCCACCACCACCACCA-CCCACCACCACCAchr13-99982753-CCCACCACCACCACCA-CCCACCACCACCACCACCAchr13-99982753-CCCACCACCACCACCA-CCCACCACCACCACCACCACCAchr13-99982753-CCCACCACCACCACCA-CCCACCACCACCACCACCACCACCA
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP3
The NM_007129.5(ZIC2):c.704_718del(p.His235_His239del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00001 in 1,596,522 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000090 ( 0 hom. )
Consequence
ZIC2
NM_007129.5 inframe_deletion
NM_007129.5 inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.61
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 Uncertain_significance. Variant got 1 ACMG points.
PP3
?
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZIC2 | NM_007129.5 | c.704_718del | p.His235_His239del | inframe_deletion | 1/3 | ENST00000376335.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZIC2 | ENST00000376335.8 | c.704_718del | p.His235_His239del | inframe_deletion | 1/3 | 1 | NM_007129.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151416Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.00000900 AC: 13AN: 1445106Hom.: 0 AF XY: 0.00000973 AC XY: 7AN XY: 719228
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ClinVar
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at