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NM_000404.3(GLB1):c.[276G>A];[75+5G>C] AND Infantile GM1 gangliosidosis

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 11, 2016
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV000234894.3

Allele description [Variation Report for NM_000404.3(GLB1):c.[276G>A];[75+5G>C]]

NM_000404.4(GLB1):c.276G>A (p.Trp92Ter)

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.276G>A (p.Trp92Ter)
HGVS:
  • NC_000003.12:g.33068940C>T
  • NG_009005.1:g.33263G>A
  • NM_000404.4:c.276G>AMANE SELECT
  • NM_001079811.3:c.186G>A
  • NM_001135602.3:c.246-3383G>A
  • NM_001317040.2:c.420G>A
  • NM_001393580.1:c.276G>A
  • NP_000395.3:p.Trp92Ter
  • NP_001073279.2:p.Trp62Ter
  • NP_001303969.2:p.Trp140Ter
  • NP_001380509.1:p.Trp92Ter
  • NC_000003.11:g.33110432C>T
  • NM_000404.2:c.276G>A
  • NM_000404.3:c.276G>A
  • p.W92X
Protein change:
W140*
Links:
dbSNP: rs748830051
NCBI 1000 Genomes Browser:
rs748830051
Molecular consequence:
  • NM_001135602.3:c.246-3383G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000404.4:c.276G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001079811.3:c.186G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001317040.2:c.420G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001393580.1:c.276G>A - nonsense - [Sequence Ontology: SO:0001587]
Functional consequence:
Unknown function

NM_000404.4(GLB1):c.75+5G>C

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.75+5G>C
HGVS:
  • NC_000003.12:g.33097006C>G
  • NG_009005.1:g.5197G>C
  • NG_009005.2:g.5140G>C
  • NG_169445.1:g.373C>G
  • NM_000404.4:c.75+5G>CMANE SELECT
  • NM_001039770.3:c.-396G>CMANE SELECT
  • NM_001135602.3:c.75+5G>C
  • NM_001136238.2:c.-292G>C
  • NM_001317040.2:c.75+5G>C
  • NM_001393580.1:c.75+5G>C
  • NC_000003.11:g.33138498C>G
  • NM_000404.3:c.75+5G>C
Links:
dbSNP: rs879253739
NCBI 1000 Genomes Browser:
rs879253739
Molecular consequence:
  • NM_001039770.3:c.-396G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001136238.2:c.-292G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000404.4:c.75+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001135602.3:c.75+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317040.2:c.75+5G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001393580.1:c.75+5G>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Infantile GM1 gangliosidosis
Synonyms:
Gangliosidosis, Generalized GM1, Type 1; GM1 gangliosidosis type 1; GM1-gangliosidosis, type I; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009260; MedGen: C0268271; Orphanet: 354; OMIM: 230500

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000268646Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics
no assertion criteria provided
Likely pathogenic
(May 11, 2016) 		germlineresearch

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Indiangermlineyes2not providednot providednot providednot providedresearch

Details of each submission

From Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics, SCV000268646.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Indian1not providednot providedresearchnot provided

Description

Variant c.75+5G>C (ENST00000307363) found to be pathogenic by online software Mutation Taster and Variant c.276G>A reported to cause disease (HGMD ID:CM115631).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 20, 2024