rs1554532014
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM5PP3
The NM_152419.3(HGSNAT):c.819T>G(p.Asn273Lys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N273I) has been classified as Likely pathogenic.
Frequency
Consequence
NM_152419.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HGSNAT | NM_152419.3 | c.819T>G | p.Asn273Lys | missense_variant, splice_region_variant | 8/18 | ENST00000379644.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HGSNAT | ENST00000379644.9 | c.819T>G | p.Asn273Lys | missense_variant, splice_region_variant | 8/18 | 2 | NM_152419.3 | P3 | |
HGSNAT | ENST00000520704.1 | c.*268T>G | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 9/10 | 1 | ||||
HGSNAT | ENST00000522082.5 | c.60T>G | p.Asn20Lys | missense_variant, splice_region_variant | 1/6 | 4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 26
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Mucopolysaccharidosis, MPS-III-C Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | May 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at