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NM_000153.4(GALC):c.1158_1161+6del

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Interpretation:
Conflicting interpretations of pathogenicity​

Pathogenic(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Nov 19, 2021)
Last evaluated:
Mar 2, 2020
Accession:
VCV000444335.11
Variation ID:
444335
Description:
10bp deletion
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NM_000153.4(GALC):c.1158_1161+6del

Allele ID
437975
Variant type
Deletion
Variant length
10 bp
Cytogenetic location
14q31.3
Genomic location
14: 87963378-87963387 (GRCh38) GRCh38 UCSC
14: 88429722-88429731 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000014.8:g.88429726_88429735del
NC_000014.9:g.87963382_87963391del
NG_011853.2:g.35177_35186del
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000014.9:87963377:GTTTACCATGGTTT:GTTT
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA7297138
dbSNP: rs759068540
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, multiple submitters, no conflicts Mar 2, 2020 RCV001044546.2
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Feb 1, 2017 RCV000513102.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GALC - - GRCh38
GRCh37
715 736

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Feb 01, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV000608710.11
Submitted: (Jul 04, 2021)
Evidence details
Pathogenic
(Aug 17, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000701445.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(Dec 13, 2019)
criteria provided, single submitter
Method: clinical testing
Galactosylceramide beta-galactosidase deficiency
Allele origin: germline
Invitae
Accession: SCV001208350.1
Submitted: (Feb 06, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This variant results in the deletion of part of exon 10 (c.1158_1161+6del) of the GALC gene. It is expected to disrupt RNA splicing and likely … (more)
Pathogenic
(Mar 02, 2020)
criteria provided, single submitter
Method: clinical testing
Galactosylceramide beta-galactosidase deficiency
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001339011.1
Submitted: (Apr 29, 2020)
Evidence details
Publications
PubMed (2)
Comment:
Variant summary: GALC c.1158_1161+6del10 is located in the end of exon 10 including a canonical splice-site at intron 10 and is predicted to affect mRNA … (more)
Pathogenic
(Sep 23, 2019)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
PerkinElmer Genomics
Accession: SCV002024144.1
Submitted: (Nov 19, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Early progression of Krabbe disease in patients with symptom onset between 0 and 5 months. Beltran-Quintero ML Orphanet journal of rare diseases 2019 PMID: 30777126
Early infantile Krabbe disease: results of the World-Wide Krabbe Registry. Duffner PK Pediatric neurology 2011 PMID: 21824559
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GALC - - - -

Text-mined citations for rs759068540...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 28, 2021