3-50320300-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_003773.5(HYAL2):c.190G>A(p.Ala64Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000372 in 1,613,946 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Consequence
NM_003773.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HYAL2 | NM_003773.5 | c.190G>A | p.Ala64Thr | missense_variant | Exon 2 of 4 | ENST00000357750.9 | NP_003764.3 | |
HYAL2 | NM_033158.5 | c.190G>A | p.Ala64Thr | missense_variant | Exon 3 of 5 | NP_149348.2 | ||
HYAL2 | XM_005265524.3 | c.190G>A | p.Ala64Thr | missense_variant | Exon 3 of 5 | XP_005265581.1 | ||
HYAL2 | XM_005265525.3 | c.190G>A | p.Ala64Thr | missense_variant | Exon 2 of 4 | XP_005265582.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152268Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461678Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727146
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152268Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74390
ClinVar
Submissions by phenotype
HYAL2 deficiency Pathogenic:1
From Fasham et al 2021 (Supplementary Table S3): At extremely low frequency in gnomAD databases In trans with p.(Arg378Cys) Cosegregation with disease in multiple affected family members (≤1/16) In silico missense prediction tools support a deleterious effect on the gene or gene product A strong consensus supporting a clinical diagnosis with a specific phenotype -
MUGGENTHALER-CHOWDHURY-CHIOZA SYNDROME Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at