NM_003719.5(PDE8B):c.895G>T (p.Glu299Ter) AND Mucopolysaccharidosis type 1

delete

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 26, 2024
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV004527044.1

Allele description

NM_003719.5(PDE8B):c.895G>T (p.Glu299Ter)

Gene:

PDE8B:phosphodiesterase 8B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q13.3

Genomic location:

Preferred name:

NM_003719.5(PDE8B):c.895G>T (p.Glu299Ter)

HGVS:

NC_000005.10:g.77349437G>T
NG_023364.2:g.174186G>T
NM_001029851.4:c.876+4506G>T
NM_001029852.4:c.895G>T
NM_001029853.4:c.835G>T
NM_001029854.4:c.877-1628G>T
NM_001349748.3:c.892G>T
NM_001349749.3:c.958G>T
NM_001349750.3:c.655G>T
NM_001349751.3:c.892G>T
NM_001349752.3:c.589G>T
NM_001349753.2:c.523G>T
NM_001376062.1:c.592G>T
NM_001376063.1:c.895G>T
NM_001376064.1:c.895G>T
NM_001376065.1:c.873+4506G>T
NM_001376066.1:c.532G>T
NM_001376067.1:c.523G>T
NM_001376068.1:c.523G>T
NM_001376069.1:c.634-1628G>T
NM_001376070.1:c.574-1628G>T
NM_001376071.1:c.571-1628G>T
NM_001376072.1:c.592G>T
NM_001376073.1:c.573+4506G>T
NM_001376074.1:c.513+4506G>T
NM_001376075.1:c.504+4506G>T
NM_001414622.1:c.523G>T
NM_001414623.1:c.523G>T
NM_003719.5:c.895G>TMANE SELECT
NP_001025023.1:p.Glu299Ter
NP_001025024.1:p.Glu279Ter
NP_001336677.1:p.Glu298Ter
NP_001336678.1:p.Glu320Ter
NP_001336679.1:p.Glu219Ter
NP_001336680.1:p.Glu298Ter
NP_001336681.1:p.Glu197Ter
NP_001336682.1:p.Glu175Ter
NP_001362991.1:p.Glu198Ter
NP_001362992.1:p.Glu299Ter
NP_001362993.1:p.Glu299Ter
NP_001362995.1:p.Glu178Ter
NP_001362996.1:p.Glu175Ter
NP_001362997.1:p.Glu175Ter
NP_001363001.1:p.Glu198Ter
NP_001401551.1:p.Glu175Ter
NP_001401552.1:p.Glu175Ter
NP_003710.1:p.Glu299Ter
NC_000005.9:g.76645262G>T

Protein change:

E175*

Molecular consequence:

NM_001029851.4:c.876+4506G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001029854.4:c.877-1628G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001376065.1:c.873+4506G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001376069.1:c.634-1628G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001376070.1:c.574-1628G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001376071.1:c.571-1628G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001376073.1:c.573+4506G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001376074.1:c.513+4506G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001376075.1:c.504+4506G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001029852.4:c.895G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001029853.4:c.835G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001349748.3:c.892G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001349749.3:c.958G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001349750.3:c.655G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001349751.3:c.892G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001349752.3:c.589G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001349753.2:c.523G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001376062.1:c.592G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001376063.1:c.895G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001376064.1:c.895G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001376066.1:c.532G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001376067.1:c.523G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001376068.1:c.523G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001376072.1:c.592G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001414622.1:c.523G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001414623.1:c.523G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_003719.5:c.895G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Mucopolysaccharidosis type 1
Synonyms:: Mucopolysaccharidosis type I; MPS 1; Attenuated MPS I (subtype); See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0001586; MedGen: C0023786

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005039079	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Pathogenic (Mar 26, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005039079

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Pathogenic
(Mar 26, 2024)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV005039079.1

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

Description

Variant summary: IDUA c.895G>T (p.Glu299X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant was absent in 191150 control chromosomes. c.895G>T has been reported in the literature in individuals affected with Mucopolysaccharidosis Type 1. These data indicate that the variant may be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic.

#	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: Sep 1, 2024

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