NM_000153.4(GALC):c.1472del (p.Lys491fs) AND not provided

Clinical significance:Pathogenic (Last evaluated: Oct 19, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001541362.2

Allele description [Variation Report for NM_000153.4(GALC):c.1472del (p.Lys491fs)]

NM_000153.4(GALC):c.1472del (p.Lys491fs)

Gene:
GALC:galactosylceramidase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
14q31.3
Genomic location:
Preferred name:
NM_000153.4(GALC):c.1472del (p.Lys491fs)
HGVS:
  • NC_000014.9:g.87947746del
  • NG_011853.2:g.50819del
  • NM_000153.4:c.1472delMANE SELECT
  • NM_001201401.1:c.1403del
  • NM_001201402.1:c.1394del
  • NP_000144.2:p.Lys491fs
  • NP_001188330.1:p.Lys468fs
  • NP_001188331.1:p.Lys465fs
  • NC_000014.8:g.88414089del
  • NC_000014.8:g.88414090del
  • NM_000153.3:c.1472del
  • NM_000153.3:c.1472delA
Protein change:
K465fs
Links:
dbSNP: rs771489305
NCBI 1000 Genomes Browser:
rs771489305
Molecular consequence:
  • NM_000153.4:c.1472del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001201401.1:c.1403del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001201402.1:c.1394del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001759350GeneDxcriteria provided, single submitter
Pathogenic
(Oct 19, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV001759350.1

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

Description

Functional studies of this variant transfected into COS1 cells showed only residual GALC activity that was comparable to mock transfected cells (reported using alternate nomenclature) (Saavedra-Matiz et al., 2016); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 27638593, 9338580)

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

Last Updated: Sep 23, 2021

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