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NM_001199397.3(NEK1):c.1769_1770del (p.Arg590fs) AND Short-rib thoracic dysplasia 6 with or without polydactyly

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Jun 1, 2017
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:
RCV000516096.2

Allele description [Variation Report for NM_001199397.3(NEK1):c.1769_1770del (p.Arg590fs)]

NM_001199397.3(NEK1):c.1769_1770del (p.Arg590fs)

Gene:
NEK1:NIMA related kinase 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
4q33
Genomic location:
Preferred name:
NM_001199397.3(NEK1):c.1769_1770del (p.Arg590fs)
HGVS:
  • NC_000004.12:g.169508311_169508312del
  • NG_027982.1:g.109316_109317del
  • NM_001199397.3:c.1769_1770delMANE SELECT
  • NM_001199398.3:c.1637_1638del
  • NM_001199399.3:c.1478_1479del
  • NM_001199400.3:c.1553_1554del
  • NM_001374418.1:c.1769_1770del
  • NM_001374419.1:c.1685_1686del
  • NM_001374420.1:c.1634_1635del
  • NM_001374421.1:c.1559_1560del
  • NM_012224.4:c.1685_1686del
  • NP_001186326.1:p.Arg590fs
  • NP_001186327.1:p.Arg546fs
  • NP_001186328.1:p.Arg493fs
  • NP_001186329.1:p.Arg518fs
  • NP_001361347.1:p.Arg590fs
  • NP_001361348.1:p.Arg562fs
  • NP_001361349.1:p.Arg545fs
  • NP_001361350.1:p.Arg520fs
  • NP_036356.1:p.Arg562fs
  • NC_000004.11:g.170429462_170429463del
  • NM_001199397.1:c.1769_1770delGG
  • NR_164630.1:n.2231_2232del
Protein change:
R493fs
Links:
dbSNP: rs1554053289
NCBI 1000 Genomes Browser:
rs1554053289
Molecular consequence:
  • NM_001199397.3:c.1769_1770del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001199398.3:c.1637_1638del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001199399.3:c.1478_1479del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001199400.3:c.1553_1554del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374418.1:c.1769_1770del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374419.1:c.1685_1686del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374420.1:c.1634_1635del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001374421.1:c.1559_1560del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_012224.4:c.1685_1686del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_164630.1:n.2231_2232del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Short-rib thoracic dysplasia 6 with or without polydactyly (SRTD6)
Synonyms:
POLYDACTYLY WITH NEONATAL CHONDRODYSTROPHY, TYPE II; Polydactyly with neonatal chondrodystrophy type 2; Majewski Syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009894; MedGen: C0024507; OMIM: 263520

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000612096Dan Cohn Lab, University Of California Los Angeles
no assertion criteria provided
Pathogenic
(Jun 1, 2017)
unknownresearch

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

SCV001479755University of Washington Center for Mendelian Genomics, University of Washington
no assertion criteria provided
Likely pathogenicinheritedresearch

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedinheritedyesnot providednot providednot providednot providednot providedresearch
not providedunknownyesnot providednot providednot providednot providednot providedresearch

Citations

PubMed

Expanding the genetic architecture and phenotypic spectrum in the skeletal ciliopathies.

Zhang W, Taylor SP, Ennis HA, Forlenza KN, Duran I, Li B, Sanchez JAO, Nevarez L, Nickerson DA, Bamshad M; University of Washington Center for Mendelian Genomics., Lachman RS, Krakow D, Cohn DH.

Hum Mutat. 2018 Jan;39(1):152-166. doi: 10.1002/humu.23362. Epub 2017 Nov 6.

PubMed [citation]
PMID:
29068549
PMCID:
PMC6198324

Details of each submission

From Dan Cohn Lab, University Of California Los Angeles, SCV000612096.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From University of Washington Center for Mendelian Genomics, University of Washington, SCV001479755.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 23, 2022