5-150521392-GC-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001543.5(NDST1):​c.141delC​(p.Ser48ArgfsTer131) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 32)

Consequence

NDST1
NM_001543.5 frameshift

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.97
Variant links:
Genes affected
NDST1 (HGNC:7680): (N-deacetylase and N-sulfotransferase 1) This gene encodes a member of the heparan sulfate/heparin GlcNAc N-deacetylase/ N-sulfotransferase family. The encoded enzyme is a type II transmembrane protein that resides in the Golgi apparatus. The encoded protein catalyzes the transfer of sulfate from 3'-phosphoadenosine 5'-phosphosulfate to nitrogen of glucosamine in heparan sulfate. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NDST1NM_001543.5 linkc.141delC p.Ser48ArgfsTer131 frameshift_variant Exon 2 of 15 ENST00000261797.7 NP_001534.1 P52848-1A8K8T3
NDST1NM_001301063.2 linkc.141delC p.Ser48ArgfsTer131 frameshift_variant Exon 2 of 14 NP_001287992.1 P52848-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NDST1ENST00000261797.7 linkc.141delC p.Ser48ArgfsTer131 frameshift_variant Exon 2 of 15 1 NM_001543.5 ENSP00000261797.6 P52848-1
NDST1ENST00000523767.5 linkc.141delC p.Ser48ArgfsTer131 frameshift_variant Exon 2 of 14 2 ENSP00000428604.1 P52848-3
NDST1ENST00000519157.1 linkc.141delC p.Ser48ArgfsTer111 frameshift_variant Exon 2 of 2 5 ENSP00000427813.1 E5RG58
NDST1ENST00000522491.1 linkc.141delC p.Ser48ArgfsTer20 frameshift_variant Exon 2 of 2 2 ENSP00000429966.1 E5RGN9

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Uncertain:1
Sep 11, 2024
GeneDx
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Not observed at significant frequency in large population cohorts (gnomAD); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is not an established mechanism of disease; Has not been previously published as pathogenic or benign to our knowledge -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-149900954; API