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NM_033116.6(NEK9):c.1489C>T (p.Arg497Ter) AND Lethal congenital contracture syndrome 10

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 18, 2019
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:
RCV000234925.1

Allele description

NM_033116.6(NEK9):c.1489C>T (p.Arg497Ter)

Gene:
NEK9:NIMA related kinase 9 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q24.3
Genomic location:
Preferred name:
NM_033116.6(NEK9):c.1489C>T (p.Arg497Ter)
HGVS:
  • NC_000014.9:g.75106541G>A
  • NG_051093.1:g.25540C>T
  • NM_001329237.2:c.1489C>T
  • NM_001329238.2:c.1135C>T
  • NM_033116.6:c.1489C>TMANE SELECT
  • NP_001316166.1:p.Arg497Ter
  • NP_001316167.1:p.Arg379Ter
  • NP_149107.4:p.Arg497Ter
  • NC_000014.8:g.75573244G>A
  • NM_033116.4:c.1489C>T
  • NM_033116.5:c.1489C>T
Protein change:
R379*; ARG497TER
Links:
OMIM: 609798.0001; dbSNP: rs757011098
NCBI 1000 Genomes Browser:
rs757011098
Molecular consequence:
  • NM_001329237.2:c.1489C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001329238.2:c.1135C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_033116.6:c.1489C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Lethal congenital contracture syndrome 10 (LCCS10)
Identifiers:
MONDO: MONDO:0014870; MedGen: C4310760; OMIM: 617022

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000292250OMIM
no assertion criteria provided
Pathogenic
(Dec 18, 2019) 		germlineliterature only

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Recessive NEK9 mutation causes a lethal skeletal dysplasia with evidence of cell cycle and ciliary defects.

Casey JP, Brennan K, Scheidel N, McGettigan P, Lavin PT, Carter S, Ennis S, Dorkins H, Ghali N, Blacque OE, Mc Gee MM, Murphy H, Lynch SA.

Hum Mol Genet. 2016 May 1;25(9):1824-35. doi: 10.1093/hmg/ddw054. Epub 2016 Feb 21.

PubMed [citation]
PMID:
26908619

Details of each submission

From OMIM, SCV000292250.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In 2 Irish Traveller families in which 5 offspring had lethal congenital contracture syndrome-10 (LCCS10; 617022), Casey et al. (2016) identified homozygosity for a c.1489C-T transition (c.1489C-T, NM_033116.4), resulting in an arg497-to-ter (R497X) substitution. The mutation segregated with disease in both families. The mutant protein was predicted to lack the majority of the RCC1-like domain, with complete loss of the NEK6 interaction region and the coiled-coil domain. Analysis of patient fibroblasts showed a significant reduction in proliferation compared to controls, as well as a reduction in the level of cells reentering S-phase, consistent with delayed cell cycle progression. Patient fibroblasts also displayed a significant reduction in cilia number and length compared to controls.

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

Last Updated: Apr 18, 2020