NM_000203.5(IDUA):c.713T>A (p.Leu238Gln) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Aug 31, 2022
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:: RCV000256027.8

Allele description [Variation Report for NM_000203.5(IDUA):c.713T>A (p.Leu238Gln)]

NM_000203.5(IDUA):c.713T>A (p.Leu238Gln)

Gene:

IDUA:alpha-L-iduronidase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4p16.3

Genomic location:

Preferred name:

NM_000203.5(IDUA):c.713T>A (p.Leu238Gln)

HGVS:

NC_000004.12:g.1001802T>A
NG_008103.1:g.19806T>A
NM_000203.5:c.713T>AMANE SELECT
NM_001363576.1:c.317T>A
NP_000194.2:p.Leu238Gln
NP_001350505.1:p.Leu106Gln
LRG_1277t1:c.713T>A
LRG_1277:g.19806T>A
LRG_1277p1:p.Leu238Gln
NC_000004.11:g.995590T>A
NM_000203.3:c.713T>A
NM_000203.4:c.713T>A
NM_000203.5(IDUA):c.713T>AMANE SELECT
NR_110313.1:n.801T>A
P35475:p.Leu238Gln

Protein change:

L106Q

Links:

UniProtKB: P35475#VAR_020980; dbSNP: rs148789453

NCBI 1000 Genomes Browser:

rs148789453

Molecular consequence:

NM_000203.5:c.713T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001363576.1:c.317T>A - missense variant - [Sequence Ontology: SO:0001583]
NR_110313.1:n.801T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV000322294	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Aug 31, 2022)	germline	clinical testing	Citation Link,
SCV002023100	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 7, 2020)	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

SCV000322294

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Aug 31, 2022)

germline

clinical testing

Citation Link,

SCV002023100

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Nov 7, 2020)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	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 GeneDx, SCV000322294.9

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

Description

Published functional studies demonstrate that the L238Q variant causes reduced IDUA activity and protein levels when expressed in Chinese hamster ovary (CHO) cells (Yogalingam et al., 2004); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 15300847, 24368159, 26260077, 31194252)

#	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, SCV002023100.3

#	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: Oct 13, 2024

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