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NM_000404.4(GLB1):c.62C>T (p.Thr21Met) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 15, 2022
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:
RCV002885921.2

Allele description [Variation Report for NM_000404.4(GLB1):c.62C>T (p.Thr21Met)]

NM_000404.4(GLB1):c.62C>T (p.Thr21Met)

Genes:
LOC129936434:ATAC-STARR-seq lymphoblastoid silent region 14182 [Gene]
GLB1:galactosidase beta 1 [Gene - OMIM - HGNC]
TMPPE:transmembrane protein with metallophosphoesterase domain [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p22.3
Genomic location:
Preferred name:
NM_000404.4(GLB1):c.62C>T (p.Thr21Met)
HGVS:
  • NC_000003.12:g.33097024G>A
  • NG_009005.2:g.5122C>T
  • NG_169445.1:g.391G>A
  • NM_000404.4:c.62C>TMANE SELECT
  • NM_001039770.3:c.-414C>TMANE SELECT
  • NM_001135602.3:c.62C>T
  • NM_001136238.2:c.-310C>T
  • NM_001317040.2:c.62C>T
  • NM_001393580.1:c.62C>T
  • NP_000395.3:p.Thr21Met
  • NP_001129074.2:p.Thr21Met
  • NP_001303969.2:p.Thr21Met
  • NP_001380509.1:p.Thr21Met
  • NC_000003.11:g.33138516G>A
  • NG_009005.1:g.5179C>T
Protein change:
T21M
Molecular consequence:
  • NM_001039770.3:c.-414C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001136238.2:c.-310C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000404.4:c.62C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001135602.3:c.62C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317040.2:c.62C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001393580.1:c.62C>T - missense variant - [Sequence Ontology: SO:0001583]

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003243165Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 15, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003243165.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 21 of the GLB1 protein (p.Thr21Met). This variant is present in population databases (rs749823446, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with GLB1-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt GLB1 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024