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NM_016604.4(KDM3B):c.1679G>A (p.Ser560Asn) AND Inborn genetic diseases

Germline classification:
Likely benign (1 submission)
Last evaluated:
Apr 13, 2022
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:
RCV002727651.2

Allele description [Variation Report for NM_016604.4(KDM3B):c.1679G>A (p.Ser560Asn)]

NM_016604.4(KDM3B):c.1679G>A (p.Ser560Asn)

Gene:
KDM3B:lysine demethylase 3B [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q31.2
Genomic location:
Preferred name:
NM_016604.4(KDM3B):c.1679G>A (p.Ser560Asn)
HGVS:
  • NC_000005.10:g.138391311G>A
  • NM_016604.4:c.1679G>AMANE SELECT
  • NP_057688.3:p.Ser560Asn
  • NC_000005.9:g.137727000G>A
  • NM_016604.3:c.1679G>A
Protein change:
S560N
Molecular consequence:
  • NM_016604.4:c.1679G>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
SCV003547375Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Apr 13, 2022) 		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, SCV003547375.2

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: May 1, 2024