rs199538589

Positions:

• chr2-128268254-G-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_Strong BP6 BS2

The NM_004807.3(HS6ST1):​c.1144C>T​(p.Arg382Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0012 in 1,611,496 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R382Q) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0010 (2 hom., cov: 34)
  • Exomes 𝑓: 0.0012 (19 hom.)
• Consequence: HS6ST1 NM_004807.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:2 B:5 O:1
• Conservation: PhyloP100: 5.54

Genes affected

HS6ST1 (HGNC:5201): (heparan sulfate 6-O-sulfotransferase 1) The protein encoded by this gene is a member of the heparan sulfate biosynthetic enzyme family. Heparan sulfate biosynthetic enzymes are key components in generating a myriad of distinct heparan sulfate fine structures that carry out multiple biological activities. This enzyme is a type II integral membrane protein and is responsible for 6-O-sulfation of heparan sulfate. This enzyme does not share significant sequence similarity with other known sulfotransferases. A pseudogene located on chromosome 1 has been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.018632412).
• BP6: Variant 2-128268254-G-A is Benign according to our data. Variant chr2-128268254-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 180161.We mark this variant Likely_benign, oryginal submissions are: {Benign=4, Likely_benign=1, Uncertain_significance=2, Likely_pathogenic=1}.
• BS2: High Homozygotes in GnomAd4 at 2 AD,AR,Digenic,Multigenic gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HS6ST1	NM_004807.3	c.1144C>T	p.Arg382Trp	missense_variant	2/2	ENST00000259241.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HS6ST1	ENST00000259241.7	c.1144C>T	p.Arg382Trp	missense_variant	2/2	1	NM_004807.3	P1
HS6ST1	ENST00000469019.1	n.361-21729C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.000992 AC: 151 AN: 152180 Hom.: 2 Cov.: 34

Gnomad AFR AF: 0.000869

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000654

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0120

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000485

Gnomad OTH AF: 0.000480

GnomAD3 exomes AF: 0.00188 AC: 464 AN: 246850 Hom.: 3 AF XY: 0.00251 AC XY: 337 AN XY: 134514

Gnomad AFR exome AF: 0.000524

Gnomad AMR exome AF: 0.000900

Gnomad ASJ exome AF: 0.00351

Gnomad EAS exome AF: 0.0000558

Gnomad SAS exome AF: 0.0110

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000440

Gnomad OTH exome AF: 0.000501

GnomAD4 exome AF: 0.00122 AC: 1774 AN: 1459198 Hom.: 19 Cov.: 32 AF XY: 0.00155 AC XY: 1128 AN XY: 725838

Gnomad4 AFR exome AF: 0.000628

Gnomad4 AMR exome AF: 0.000783

Gnomad4 ASJ exome AF: 0.00322

Gnomad4 EAS exome AF: 0.000277

Gnomad4 SAS exome AF: 0.0118

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000455

Gnomad4 OTH exome AF: 0.00133

GnomAD4 genome AF: 0.000998 AC: 152 AN: 152298 Hom.: 2 Cov.: 34 AF XY: 0.00125 AC XY: 93 AN XY: 74468

Gnomad4 AFR AF: 0.000890

Gnomad4 AMR AF: 0.000654

Gnomad4 ASJ AF: 0.00259

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0122

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000485

Gnomad4 OTH AF: 0.000475

Alfa AF: 0.00114 Hom.: 0

Bravo AF: 0.000767

ESP6500AA AF: 0.000731 AC: 3

ESP6500EA AF: 0.000358 AC: 3

ExAC AF: 0.00213 AC: 257

EpiCase AF: 0.000436

EpiControl AF: 0.000533

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:2 Benign:5 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:1 Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Invitae	Nov 27, 2023	- -
Uncertain significance, flagged submission	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The HS6ST1 p.R382W variant was identified in 5 of 1590 proband chromosomes (frequency: 0.00314) from individuals or families with idiopathic hypogonadotropic hypogonadism (Zhu_2015_PMID:25636053, Miraoui_2013_PMID:23643382, Tornberg_2011_PMID:21700882). The variant was identified in dbSNP (ID: rs199538589) and in ClinVar (classified as likely pathogenic by the Chan Lab at Boston Children's Hospital and benign by Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine with the associated condition of hypogonadotrophic hypogonadism). The variant was also identified in control databases in 480 of 278216 chromosomes (3 homozygous) at a frequency of 0.001725 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: South Asian in 337 of 30560 chromosomes (freq: 0.01103), Ashkenazi Jewish in 35 of 10268 chromosomes (freq: 0.003409), Latino in 31 of 35288 chromosomes (freq: 0.000879), African in 16 of 23958 chromosomes (freq: 0.000668), European (non-Finnish) in 56 of 126664 chromosomes (freq: 0.000442), Other in 3 of 7078 chromosomes (freq: 0.000424) and East Asian in 2 of 19480 chromosomes (freq: 0.000103), but was not observed in the European (Finnish) population. The p.Arg382 residue is conserved in mammals but not in more distantly related organisms, and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In vitro functional analysis demonstrated a 25 to 35% reduction in enzymatic activity with the p.R382W mutant compared to wildtype, and in an in vivo assay involving C. elegans, the p.R382W mutant displayed a reduced capacity to rescue a kal1-dependent axon branching phenotype compared to wildtype HS6ST1 (Tornberg_2011_PMID:21700882). Tornberg et al. (2011) identified the p.R382W variant in three unrelated individuals with hypogonadotropic hypogonadism: a female and two males (1 with anosmia and 2 with a normal sense of smell). The female proband had a brother with delayed puberty who did not carry the HS6ST1 p.R382W mutation, whereas the anosmic male proband had an unaffected brother who did carry the mutation, indicating that the variant did not segregate with disease (Tornberg_2011_PMID:21700882). In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign. -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 24, 2020	This variant is associated with the following publications: (PMID: 21700882, 23643382, 26207952, 27535533, 30669598) -

Hypogonadotropic hypogonadism 7 with or without anosmia Pathogenic:1 Benign:1

Benign, criteria provided, single submitter	clinical testing	Mendelics	Aug 22, 2023	- -
Likely pathogenic, flagged submission	case-control	Chan Lab, Boston Children's Hospital	Nov 01, 2014	- -

HS6ST1-related disorder Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 20, 2023

The HS6ST1 c.1144C>T variant is predicted to result in the amino acid substitution p.Arg382Trp. This variant has been reported in multiple unrelated patients with hypogonadotropic hypogonadism (referred to as R372W in Tornberg et al. 2011. PubMed ID: 21700882; Miraoui et al. 2013. PubMed ID: 23643382; Zhu et al. 2015. PubMed ID: 25636053), and was defined as a founder allele in Caucasian and South Asian ethnicities (Choi et al. 2015. PubMed ID: 26207952, Table 2). In vitro and in vivo functional studies showed that the p.Arg382Trp variant resulted in reduced enzymatic activity compared to wild-type (referred to as R372W in Tornberg et al. 2011. PubMed ID: 21700882). However, this variant is found at an allele frequency of up to ~1.12% in South Asian individuals (including 3 homozygotes) in a large population database of individuals with unknown phenotype, which is likely too common to be a primary cause of autosomal dominant disease. Of note, in a recent publication, this variant was found in a patient with milder adult-onset form of hypogonadotropic hypogonadism (Cangiano et al. 2019. PubMed ID: 30669598, Table S1). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency, unrelated to patient disease -

Hypogonadotropic hypogonadism 15 with or without anosmia Benign:1

Benign, criteria provided, single submitter

research

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

-

The heterozygous p.Arg382Trp variant in HS6ST1 has been identified in 6 individuals with idiopathic hypogonadotropic hypogonadism (PMID: 21700882, 23643382), and has been identified in >1% of South Asian chromosomes and 4 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In vitro functional studies provide some evidence that the p.Arg382Trp variant may silghtly impact protein function (PMID: 21700882). However, these types of assays may not accurately represent biological function. In summary, this variant meets criteria to be classified as benign for autosomal dominant idiopathic hypogonadotropic hypogonadism. -

HYPOGONADOTROPIC HYPOGONADISM 15 WITH OR WITHOUT ANOSMIA, SUSCEPTIBILITY TO Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Jul 12, 2011

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.29
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Uncertain	0.070
CADD	Pathogenic	29
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.49	T
Eigen	Uncertain	0.41
Eigen_PC	Uncertain	0.35
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.94	D
MetaRNN	Benign	0.019	T
MetaSVM	Uncertain	0.39	D
MutationAssessor	Uncertain	2.1	M
MutationTaster	Benign	0.99	D
PrimateAI	Pathogenic	0.84	D
PROVEAN	Uncertain	-2.8	D
REVEL	Uncertain	0.63
Sift	Uncertain	0.0020	D
Sift4G	Uncertain	0.0020	D
Polyphen		1.0	D
Vest4		0.85
MVP		0.82
ClinPred		0.027	T
GERP RS		4.5
Varity_R		0.20
gMVP		0.50

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

Other links and lift over

dbSNP: rs199538589; hg19: chr2-129025828;