chr3-57198277-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM5PP3_StrongPP5
The NM_003865.3(HESX1):c.478C>T(p.Arg160Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000185 in 1,460,524 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R160H) has been classified as Likely pathogenic.
Frequency
Consequence
NM_003865.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HESX1 | NM_003865.3 | c.478C>T | p.Arg160Cys | missense_variant | 4/4 | ENST00000295934.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HESX1 | ENST00000295934.8 | c.478C>T | p.Arg160Cys | missense_variant | 4/4 | 1 | NM_003865.3 | P1 | |
HESX1 | ENST00000647958.1 | c.478C>T | p.Arg160Cys | missense_variant | 7/7 | P1 | |||
HESX1 | ENST00000473921.2 | c.376C>T | p.Arg126Cys | missense_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250912Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135754
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1460524Hom.: 0 Cov.: 30 AF XY: 0.0000206 AC XY: 15AN XY: 726566
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Septo-optic dysplasia sequence Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 1998 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at