NM_000203.5(IDUA):c.46_57del (p.Ser16_Ala19del) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: May 22, 2025
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000173083.23

Allele description [Variation Report for NM_000203.5(IDUA):c.46_57del (p.Ser16_Ala19del)]

NM_000203.5(IDUA):c.46_57del (p.Ser16_Ala19del)

Genes:

IDUA:alpha-L-iduronidase [Gene - OMIM - HGNC]
SLC26A1:solute carrier family 26 member 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

4p16.3

Genomic location:

Preferred name:

NM_000203.5(IDUA):c.46_57del (p.Ser16_Ala19del)

Other names:

NM_000203.5(IDUA):c.46_57del; p.Ser16_Ala19del

HGVS:

NC_000004.12:g.987130_987141del
NG_008103.1:g.5134_5145del
NG_033042.1:g.11307_11318del
NG_158244.2:g.330_341del
NM_000203.5:c.46_57delMANE SELECT
NM_134425.4:c.576+3998_576+4009del
NP_000194.2:p.Ser16_Ala19del
LRG_1277t1:c.46_57del
LRG_1277:g.5134_5145del
LRG_1277p1:p.Ser16_Ala19del
NC_000004.11:g.980907_980918del
NC_000004.11:g.980918_980929del
NM_000203.3:c.46_57del
NM_000203.3:c.46_57delTCGCTCCTGGCC
NM_000203.4:c.46_57del
NM_000203.4:c.46_57del12
NM_000203.4:c.46_57delTCGCTCCTGGCC
NM_000203.5:c.46_57del12MANE SELECT
NR_110313.1:n.134_145del

Links:

dbSNP: rs398123260

Molecular consequence:

NM_000203.5:c.46_57del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_134425.4:c.576+3998_576+4009del - intron variant - [Sequence Ontology: SO:0001627]
NR_110313.1:n.134_145del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000224167	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions)	Pathogenic (Mar 22, 2016)	germline	clinical testing	Citation Link,
SCV001773949	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Mar 18, 2025)	germline	clinical testing	Citation Link,
SCV002023101	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 22, 2025)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000224167

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions)

Pathogenic
(Mar 22, 2016)

germline

clinical testing

Citation Link,

SCV001773949

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Mar 18, 2025)

germline

clinical testing

Citation Link,

SCV002023101

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(May 22, 2025)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	12	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Eurofins Ntd Llc (ga), SCV000224167.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	12	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		12	not provided	not provided	not provided

From GeneDx, SCV001773949.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

In-frame deletion of 4 of amino acid(s)in a non-repeat region predicted to critically alter the protein; In silico analysis supports a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 23786846, 15300847, 28604952, 21734815, 25098213, 7951228, 11735025, 21394825, Fenton-Navarro2017[CaseReport], 12189649, 37218880, 34813777, 30548430, 21480867)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV002023101.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jul 14, 2026

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