X-149482765-A-G

Variant names:

• chrX-149482765-A-G
• rs1064458
• NM_000202.8:c.1634T>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_000202.8(IDS):​c.1634T>C​(p.Phe545Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: IDS NM_000202.8 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.473
• Publications: 0 publications found

Genes affected

IDS (HGNC:5389): (iduronate 2-sulfatase) This gene encodes a member of the sulfatase family of proteins. The encoded preproprotein is proteolytically processed to generate two polypeptide chains. This enzyme is involved in the lysosomal degradation of heparan sulfate and dermatan sulfate. Mutations in this gene are associated with the X-linked lysosomal storage disease mucopolysaccharidosis type II, also known as Hunter syndrome. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed. [provided by RefSeq, Jan 2016]

IDS Gene-Disease associations (from GenCC):

• mucopolysaccharidosis type 2

  Inheritance: XL, AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Genomics England PanelApp, PanelApp Australia, ClinGen, Labcorp Genetics (formerly Invitae), Myriad Women’s Health
• mucopolysaccharidosis type 2, attenuated form

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
• mucopolysaccharidosis type 2, severe form

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000241489 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.048950016).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000202.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IDS	NM_000202.8	MANE Select	c.1634T>C	p.Phe545Ser	missense	Exon 9 of 9	NP_000193.1	P22304-1
	IDS	NM_001166550.4		c.1364T>C	p.Phe455Ser	missense	Exon 9 of 9	NP_001160022.1	B4DGD7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IDS	ENST00000340855.11	TSL:1 MANE Select	c.1634T>C	p.Phe545Ser	missense	Exon 9 of 9	ENSP00000339801.6	P22304-1
	ENSG00000241489	ENST00000651111.1		c.1001T>C	p.Phe334Ser	missense	Exon 14 of 14	ENSP00000498395.1	B3KWA1
	IDS	ENST00000875674.1		c.1715T>C	p.Phe572Ser	missense	Exon 10 of 10	ENSP00000545733.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 23

ClinVar

ClinVar submissions as Germline

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.068
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.44
CADD	Benign	0.81
DANN	Benign	0.54
DEOGEN2	Benign	0.28	T
FATHMM_MKL	Benign	0.021	N
LIST_S2	Benign	0.29	T
M_CAP	Uncertain	0.093	D
MetaRNN	Benign	0.049	T
MetaSVM	Pathogenic	0.84	D
MutationAssessor	Benign	-0.90	N
PhyloP100		-0.47
PrimateAI	Benign	0.32	T
PROVEAN	Benign	0.080	N
REVEL	Benign	0.19
Sift	Benign	0.39	T
Sift4G	Benign	0.40	T
Polyphen		0.0030	B
Vest4		0.032
MutPred		0.48		Gain of disorder (P = 0.0028)
MVP		0.15
MPC		0.36
ClinPred		0.045	T
GERP RS		-2.7
Varity_R		0.27
gMVP		0.67
Mutation Taster		=91/9	polymorphism

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

Other links and lift over

dbSNP: rs1064458; hg19: chrX-148564296;