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NM_003157.6(NEK4):c.2363G>A (p.Arg788His) AND not specified

Germline classification:
Likely benign (1 submission)
Last evaluated:
Sep 1, 2021
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:
RCV004481003.1

Allele description [Variation Report for NM_003157.6(NEK4):c.2363G>A (p.Arg788His)]

NM_003157.6(NEK4):c.2363G>A (p.Arg788His)

Gene:
NEK4:NIMA related kinase 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p21.1
Genomic location:
Preferred name:
NM_003157.6(NEK4):c.2363G>A (p.Arg788His)
HGVS:
  • NC_000003.12:g.52737656C>T
  • NG_053026.1:g.38294G>A
  • NM_001193533.3:c.2096G>A
  • NM_001348412.2:c.2225G>A
  • NM_001348413.2:c.2225G>A
  • NM_001348414.2:c.2117G>A
  • NM_003157.6:c.2363G>AMANE SELECT
  • NP_001180462.1:p.Arg699His
  • NP_001335341.1:p.Arg742His
  • NP_001335342.1:p.Arg742His
  • NP_001335343.1:p.Arg706His
  • NP_003148.2:p.Arg788His
  • NC_000003.11:g.52771672C>T
  • NM_003157.4:c.2363G>A
Protein change:
R699H
Molecular consequence:
  • NM_001193533.3:c.2096G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001348412.2:c.2225G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001348413.2:c.2225G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001348414.2:c.2117G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003157.6:c.2363G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004981777Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Sep 1, 2021) 		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, SCV004981777.1

#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 7, 2024