rs387906813
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_005257.6(GATA6):c.1396A>C(p.Asn466His) 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. 12/20 in silico tools predict a damaging 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. N466D) has been classified as Pathogenic.
Frequency
Consequence
NM_005257.6 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 |
---|---|---|---|---|---|---|---|
GATA6 | NM_005257.6 | c.1396A>C | p.Asn466His | missense_variant | 4/7 | ENST00000269216.10 | |
GATA6 | XM_047437483.1 | c.1396A>C | p.Asn466His | missense_variant | 4/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA6 | ENST00000269216.10 | c.1396A>C | p.Asn466His | missense_variant | 4/7 | 1 | NM_005257.6 | P1 | |
GATA6 | ENST00000581694.1 | c.1396A>C | p.Asn466His | missense_variant | 3/6 | 1 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Persistent truncus arteriosus Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 18, 2009 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at