rs122463168
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_003413.4(ZIC3):c.763T>G(p.Trp255Gly) 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 Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. W255S) has been classified as Likely pathogenic.
Frequency
Consequence
NM_003413.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZIC3 | NM_003413.4 | c.763T>G | p.Trp255Gly | missense_variant | 1/3 | ENST00000287538.10 | |
ZIC3 | NM_001330661.1 | c.763T>G | p.Trp255Gly | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZIC3 | ENST00000287538.10 | c.763T>G | p.Trp255Gly | missense_variant | 1/3 | 1 | NM_003413.4 | P1 | |
ZIC3 | ENST00000370606.3 | c.763T>G | p.Trp255Gly | missense_variant | 1/3 | 5 |
Frequencies
GnomAD3 genomes Cov.: 25
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 25
ClinVar
Submissions by phenotype
Heterotaxy, visceral, 1, X-linked Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 15, 2008 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at