NM_000404.4(GLB1):c.1298_1299del (p.Ser433fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 11, 2021
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:: RCV001045376.4

Allele description [Variation Report for NM_000404.4(GLB1):c.1298_1299del (p.Ser433fs)]

NM_000404.4(GLB1):c.1298_1299del (p.Ser433fs)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

3p22.3

Genomic location:

Preferred name:

NM_000404.4(GLB1):c.1298_1299del (p.Ser433fs)

HGVS:

NC_000003.12:g.33018496AG[3]
NC_000003.12:g.33018496_33018497AG[3]
NG_009005.1:g.83700CT[3]
NM_000404.4:c.1298_1299delMANE SELECT
NM_001079811.3:c.1208_1209del
NM_001135602.3:c.905_906del
NM_001317040.2:c.1442_1443del
NP_000395.3:p.Ser433fs
NP_001073279.2:p.Ser403fs
NP_001129074.2:p.Ser302fs
NP_001303969.2:p.Ser481fs
NC_000003.11:g.33059988AG[3]
NC_000003.11:g.33059988_33059989del
NM_000404.2:c.1298_1299del

Protein change:

S302fs

Links:

dbSNP: rs1697335361

NCBI 1000 Genomes Browser:

rs1697335361

Molecular consequence:

NM_000404.4:c.1298_1299del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001079811.3:c.1208_1209del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001135602.3:c.905_906del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001317040.2:c.1442_1443del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV001209224	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 11, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 18524657, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001209224

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 11, 2021)

germline

clinical testing

PubMed (2)
[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

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001209224.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

ClinVar contains an entry for this variant (Variation ID: 842879). For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with GLB1-related conditions. This sequence change creates a premature translational stop signal (p.Ser433Phefs*23) in the GLB1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GLB1 are known to be pathogenic (PMID: 18524657). This variant is not present in population databases (gnomAD no frequency).

#	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: Feb 28, 2024

ClinVar

Relating variation to medicine