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NM_032590.5(KDM2B):c.1952G>A (p.Cys651Tyr) AND Inborn genetic diseases

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 13, 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:
RCV004409007.1

Allele description [Variation Report for NM_032590.5(KDM2B):c.1952G>A (p.Cys651Tyr)]

NM_032590.5(KDM2B):c.1952G>A (p.Cys651Tyr)

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.1952G>A (p.Cys651Tyr)
HGVS:
  • NC_000012.12:g.121453127C>T
  • NG_033820.1:g.132889G>A
  • NG_033820.2:g.134152G>A
  • NG_126876.1:g.303C>T
  • NM_001005366.2:c.1859G>A
  • NM_032590.5:c.1952G>AMANE SELECT
  • NP_001005366.1:p.Cys620Tyr
  • NP_115979.3:p.Cys651Tyr
  • NC_000012.11:g.121890930C>T
  • NM_032590.4:c.1952G>A
Protein change:
C620Y
Molecular consequence:
  • NM_001005366.2:c.1859G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_032590.5:c.1952G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV004891535Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Oct 13, 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, SCV004891535.1

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

Description

The c.1952G>A (p.C651Y) alteration is located in exon 13 (coding exon 13) of the KDM2B gene. This alteration results from a G to A substitution at nucleotide position 1952, causing the cysteine (C) at amino acid position 651 to be replaced by a tyrosine (Y). This variant was flagged as a low confidence call in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. This alteration is predicted to be deleterious by in silico analysis. 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