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NM_001478.5(B4GALNT1):c.263dup (p.Leu89fs) AND not provided

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
May 31, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001009218.2

Allele description [Variation Report for NM_001478.5(B4GALNT1):c.263dup (p.Leu89fs)]

NM_001478.5(B4GALNT1):c.263dup (p.Leu89fs)

Gene:
B4GALNT1:beta-1,4-N-acetyl-galactosaminyltransferase 1 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
12q13.3
Genomic location:
Preferred name:
NM_001478.5(B4GALNT1):c.263dup (p.Leu89fs)
Other names:
B4GALNT1, 1-BP DUP, 263G; p.Leu89Profs*13
HGVS:
  • NC_000012.12:g.57631327dup
  • NG_033849.1:g.6920dup
  • NM_001276468.2:c.219-234dup
  • NM_001276469.2:c.263dup
  • NM_001478.5:c.263dupMANE SELECT
  • NP_001263398.1:p.Leu89fs
  • NP_001469.1:p.Leu89fs
  • NC_000012.11:g.58025102_58025103insC
  • NC_000012.11:g.58025110dup
  • NC_000012.12:g.57631319_57631320insC
  • NM_001276469.1:c.263dupG
  • NM_001478.3:c.263dupG
  • NM_001478.4:c.263dup
  • NM_001478.4:c.263dupG
Protein change:
L89fs
Links:
OMIM: 601873.0003; dbSNP: rs745744124
NCBI 1000 Genomes Browser:
rs745744124
Molecular consequence:
  • NM_001276469.2:c.263dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001478.5:c.263dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001276468.2:c.219-234dup - intron variant - [Sequence Ontology: SO:0001627]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001169037GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Mar 15, 2019) 		germlineclinical testing

Citation Link,

SCV004227285Mayo Clinic Laboratories, Mayo Clinic
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(May 31, 2022) 		germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Citations

PubMed

Alteration of ganglioside biosynthesis responsible for complex hereditary spastic paraplegia.

Boukhris A, Schule R, Loureiro JL, Lourenço CM, Mundwiller E, Gonzalez MA, Charles P, Gauthier J, Rekik I, Acosta Lebrigio RF, Gaussen M, Speziani F, Ferbert A, Feki I, Caballero-Oteyza A, Dionne-Laporte A, Amri M, Noreau A, Forlani S, Cruz VT, Mochel F, Coutinho P, et al.

Am J Hum Genet. 2013 Jul 11;93(1):118-23. doi: 10.1016/j.ajhg.2013.05.006. Epub 2013 Jun 6.

PubMed [citation]
PMID:
23746551
PMCID:
PMC3710753

Identification of a new B4GalNAcT1 (GM2/GD2/GA2 synthase) isoform, and regulation of enzyme stability and intracellular transport by arginine-based motif.

Shishido F, Uemura S, Kashimura M, Inokuchi JI.

Biochim Biophys Acta Biomembr. 2017 Oct;1859(10):2001-2011. doi: 10.1016/j.bbamem.2017.07.006. Epub 2017 Jul 12.

PubMed [citation]
PMID:
28709807
See all PubMed Citations (7)

Details of each submission

From GeneDx, SCV001169037.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.263dupG variant in the B4GALNT1 gene has been reported previously in the homozygous state in an individual with hereditary spastic paraplegia with learning disability, lower limb spasticity and weakness, nystagmus, axonal sensitive neuropathy, white matter hyperintensities, and cerebral atrophy (Boukhris et al., 2013). The c.263dupG variant causes a frameshift starting with codon Leucine 89, changes this amino acid to a Proline residue, and creates a premature Stop codon at position 13 of the new reading frame, denoted p.Leu89ProfsX13. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.263dupG variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). We interpret c.263dupG as a likely pathogenic variant.

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

From Mayo Clinic Laboratories, Mayo Clinic, SCV004227285.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (7)

Description

PM2, PM3, PS3, PVS1

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

Last Updated: Sep 29, 2024