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

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jan 20, 2023
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:: RCV003766144.1

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)

Name:: Mucopolysaccharidosis, MPS-IV-B (MPS4B)
Synonyms:: MPS IVB; Morquio syndrome B; MPS 4B; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009660; MedGen: C0086652; Orphanet: 582; OMIM: 253010

Name:: GM1 gangliosidosis
Synonyms:: Beta galactosidase 1 deficiency; GLB 1 deficiency
Identifiers:: MONDO: MONDO:0018149; MedGen: C0085131

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004595880	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Jan 20, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 16199547, 18524657, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004595880

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Jan 20, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

GM1 gangliosidosis: review of clinical, molecular, and therapeutic aspects.

Brunetti-Pierri N, Scaglia F.

Mol Genet Metab. 2008 Aug;94(4):391-396. doi: 10.1016/j.ymgme.2008.04.012. Epub 2008 Jun 3. Review.

PubMed [citation]

PMID:: 18524657

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004595880.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 372370). This variant has not been reported in the literature in individuals affected with GLB1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 3 of the GLB1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in GLB1 are known to be pathogenic (PMID: 18524657).

#	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: Mar 5, 2024

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