5-150521397-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001543.5(NDST1):​c.143C>T​(p.Ser48Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000174 in 1,613,140 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000018 ( 0 hom. )

Consequence

NDST1
NM_001543.5 missense

Scores

3
4
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.99
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.14202553).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NDST1NM_001543.5 linkc.143C>T p.Ser48Leu missense_variant Exon 2 of 15 ENST00000261797.7 NP_001534.1 P52848-1A8K8T3
NDST1NM_001301063.2 linkc.143C>T p.Ser48Leu missense_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.143C>T p.Ser48Leu missense_variant Exon 2 of 15 1 NM_001543.5 ENSP00000261797.6 P52848-1
NDST1ENST00000523767.5 linkc.143C>T p.Ser48Leu missense_variant Exon 2 of 14 2 ENSP00000428604.1 P52848-3
NDST1ENST00000519157.1 linkc.143C>T p.Ser48Leu missense_variant Exon 2 of 2 5 ENSP00000427813.1 E5RG58
NDST1ENST00000522491.1 linkc.143C>T p.Ser48Leu missense_variant Exon 2 of 2 2 ENSP00000429966.1 E5RGN9

Frequencies

GnomAD3 genomes
AF:
0.0000131
AC:
2
AN:
152164
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000281
AC:
7
AN:
248676
Hom.:
0
AF XY:
0.0000297
AC XY:
4
AN XY:
134660
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000289
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.0000980
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000895
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000178
AC:
26
AN:
1460976
Hom.:
0
Cov.:
31
AF XY:
0.0000206
AC XY:
15
AN XY:
726862
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000447
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000756
Gnomad4 SAS exome
AF:
0.000139
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000809
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000131
AC:
2
AN:
152164
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000434
Hom.:
0
Bravo
AF:
0.00000756
ExAC
AF:
0.0000494
AC:
6

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.083
BayesDel_addAF
Benign
-0.26
T
BayesDel_noAF
Benign
-0.39
CADD
Uncertain
23
DANN
Uncertain
0.99
DEOGEN2
Benign
0.21
.;.;.;T
Eigen
Benign
-0.084
Eigen_PC
Benign
0.054
FATHMM_MKL
Uncertain
0.97
D
LIST_S2
Uncertain
0.94
D;D;D;D
M_CAP
Benign
0.0067
T
MetaRNN
Benign
0.14
T;T;T;T
MetaSVM
Benign
-0.97
T
MutationAssessor
Benign
0.87
.;.;.;L
PrimateAI
Uncertain
0.59
T
PROVEAN
Pathogenic
-5.4
D;N;N;N
REVEL
Benign
0.078
Sift
Pathogenic
0.0
D;T;T;T
Sift4G
Pathogenic
0.0
D;T;T;T
Polyphen
0.0040, 0.021
.;.;B;B
Vest4
0.20, 0.18
MutPred
0.20
Loss of glycosylation at S48 (P = 0.0122);Loss of glycosylation at S48 (P = 0.0122);Loss of glycosylation at S48 (P = 0.0122);Loss of glycosylation at S48 (P = 0.0122);
MVP
0.28
MPC
0.60
ClinPred
0.19
T
GERP RS
5.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.095
gMVP
0.31

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs754000766; hg19: chr5-149900959; COSMIC: COSV105067681; COSMIC: COSV105067681; API