5-150521467-G-C

Variant summary

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

The NM_001543.5(NDST1):ā€‹c.213G>Cā€‹(p.Lys71Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: š‘“ 0.0000066 ( 0 hom., cov: 32)
Exomes š‘“: 0.0000014 ( 0 hom. )

Consequence

NDST1
NM_001543.5 missense

Scores

6
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.88
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=0.22749776).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NDST1NM_001543.5 linkc.213G>C p.Lys71Asn missense_variant Exon 2 of 15 ENST00000261797.7 NP_001534.1 P52848-1A8K8T3
NDST1NM_001301063.2 linkc.213G>C p.Lys71Asn 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.213G>C p.Lys71Asn missense_variant Exon 2 of 15 1 NM_001543.5 ENSP00000261797.6 P52848-1
NDST1ENST00000523767.5 linkc.213G>C p.Lys71Asn missense_variant Exon 2 of 14 2 ENSP00000428604.1 P52848-3
NDST1ENST00000519157.1 linkc.213G>C p.Lys71Asn missense_variant Exon 2 of 2 5 ENSP00000427813.1 E5RG58
NDST1ENST00000522491.1 linkc.*9G>C downstream_gene_variant 2 ENSP00000429966.1 E5RGN9

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152174
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
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:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000399
AC:
1
AN:
250600
Hom.:
0
AF XY:
0.00000738
AC XY:
1
AN XY:
135558
show subpopulations
Gnomad AFR exome
AF:
0.0000621
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1461582
Hom.:
0
Cov.:
31
AF XY:
0.00000138
AC XY:
1
AN XY:
727098
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152292
Hom.:
0
Cov.:
32
AF XY:
0.0000134
AC XY:
1
AN XY:
74474
show subpopulations
Gnomad4 AFR
AF:
0.0000241
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:
0.00
Gnomad4 OTH
AF:
0.00
ExAC
AF:
0.00000824
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.35
BayesDel_addAF
Benign
-0.31
T
BayesDel_noAF
Benign
-0.50
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Benign
0.28
.;.;T
Eigen
Benign
0.049
Eigen_PC
Benign
0.053
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Uncertain
0.90
D;D;D
M_CAP
Benign
0.013
T
MetaRNN
Benign
0.23
T;T;T
MetaSVM
Benign
-0.95
T
MutationAssessor
Benign
1.4
.;.;L
PrimateAI
Uncertain
0.67
T
PROVEAN
Benign
-2.2
N;N;N
REVEL
Benign
0.085
Sift
Uncertain
0.0080
D;D;D
Sift4G
Benign
0.10
T;T;T
Polyphen
0.61
.;P;P
Vest4
0.31, 0.30
MutPred
0.20
Loss of methylation at K71 (P = 0.0084);Loss of methylation at K71 (P = 0.0084);Loss of methylation at K71 (P = 0.0084);
MVP
0.57
MPC
0.93
ClinPred
0.24
T
GERP RS
3.3
Varity_R
0.24
gMVP
0.39

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs545691216; hg19: chr5-149901029; API