NM_000404.4(GLB1):c.396+2T>C AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 28, 2015
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:: RCV000414347.1

Allele description [Variation Report for NM_000404.4(GLB1):c.396+2T>C]

NM_000404.4(GLB1):c.396+2T>C

Gene:

GLB1:galactosidase beta 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p22.3

Genomic location:

Preferred name:

NM_000404.4(GLB1):c.396+2T>C

HGVS:

NC_000003.12:g.33068818A>G
NG_009005.1:g.33385T>C
NG_009005.2:g.33328T>C
NM_000404.4:c.396+2T>CMANE SELECT
NM_001079811.3:c.306+2T>C
NM_001135602.3:c.246-3261T>C
NM_001317040.2:c.540+2T>C
NM_001393580.1:c.396+2T>C
NC_000003.11:g.33110310A>G
NM_000404.2:c.396+2T>C

Links:

dbSNP: rs1057517738

NCBI 1000 Genomes Browser:

rs1057517738

Molecular consequence:

NM_001135602.3:c.246-3261T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000404.4:c.396+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001079811.3:c.306+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001317040.2:c.540+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001393580.1:c.396+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]

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
SCV000490539	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Apr 28, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000490539

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Apr 28, 2015)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000490539.2

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

Description

The c.396+2 T>C splice site variant in the GLB1 gene destroys the canonical splice donor site in intron 3. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense -mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. Although this variant has not been previously reported to our knowledge, it is expected to be pathogenic.

#	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

Last Updated: Sep 29, 2024

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