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NM_001081.4(CUBN):c.6125-2A>G AND CUBN-related disorder

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 14, 2024
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:
RCV003422417.6

Allele description [Variation Report for NM_001081.4(CUBN):c.6125-2A>G]

NM_001081.4(CUBN):c.6125-2A>G

Gene:
CUBN:cubilin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10p13
Genomic location:
Preferred name:
NM_001081.4(CUBN):c.6125-2A>G
HGVS:
  • NC_000010.11:g.16928305T>C
  • NG_008967.1:g.206513A>G
  • NM_001081.4:c.6125-2A>GMANE SELECT
  • LRG_540t1:c.6125-2A>G
  • LRG_540:g.206513A>G
  • NC_000010.10:g.16970304T>C
  • NM_001081.3:c.6125-2A>G
Links:
dbSNP: rs75386064
NCBI 1000 Genomes Browser:
rs75386064
Molecular consequence:
  • NM_001081.4:c.6125-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:
CUBN-related disorder
Synonyms:
CUBN-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004117640PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Uncertain significance
(Feb 14, 2024) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004117640.3

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

Description

The CUBN c.6125-2A>G variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. This variant has been reported in the homozygous and compound heterozygous states in multiple individuals with kidney disease and chronic proteinuria (Bedin et al. 2020. PubMed ID: 31613795). This variant is reported in 0.69% of alleles in individuals of African descent in gnomAD, including one homozygous observation. Other loss of function and canonical splice variants have been reported as causative both up and downstream of this change; however, these all have significantly lower frequencies in the gnomAD population. Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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

Last Updated: Nov 24, 2024