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NM_032590.5(KDM2B):c.1735-1G>A AND Inborn genetic diseases

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 1, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV004409004.1

Allele description [Variation Report for NM_032590.5(KDM2B):c.1735-1G>A]

NM_032590.5(KDM2B):c.1735-1G>A

Gene:
KDM2B:lysine demethylase 2B [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q24.31
Genomic location:
Preferred name:
NM_032590.5(KDM2B):c.1735-1G>A
HGVS:
  • NC_000012.12:g.121453345C>T
  • NG_033820.1:g.132671G>A
  • NG_033820.2:g.133934G>A
  • NG_126876.1:g.521C>T
  • NM_001005366.2:c.1642-1G>A
  • NM_032590.5:c.1735-1G>AMANE SELECT
  • NC_000012.11:g.121891148C>T
  • NM_032590.4:c.1735-1G>A
Molecular consequence:
  • NM_001005366.2:c.1642-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_032590.5:c.1735-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004891532Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Dec 1, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV004891532.1

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

Description

The c.1735-1G>A intronic variant results from a G to A substitution one nucleotide before coding exon 13 of the KDM2B gene. Alterations that disrupt the canonical splice site are expected to result in aberrant splicing. The resulting transcript is predicted to be in-frame and is not expected to trigger nonsense-mediated mRNA decay; however, direct evidence is unavailable. The exact functional effect of the altered amino acid sequence is unknown. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and may result in the creation or strengthening of a novel splice acceptor site. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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

Last Updated: May 7, 2024