14-100277452-T-C
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PM5PP2PP3_ModeratePP5
The NM_003403.5(YY1):c.1097T>C(p.Leu366Pro) 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. L366V) has been classified as Pathogenic.
Frequency
Consequence
NM_003403.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YY1 | NM_003403.5 | c.1097T>C | p.Leu366Pro | missense_variant | 5/5 | ENST00000262238.10 | |
MIR6764 | NR_106822.1 | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YY1 | ENST00000262238.10 | c.1097T>C | p.Leu366Pro | missense_variant | 5/5 | 1 | NM_003403.5 | P1 | |
MIR6764 | ENST00000636393.1 | downstream_gene_variant |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Gabriele de Vries syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 17, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at