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NM_001199397.3(NEK1):c.3075C>T (p.Asn1025=) AND Short-rib thoracic dysplasia 6 with or without polydactyly

Germline classification:
Conflicting classifications of pathogenicity (2 submissions)
Last evaluated:
Jan 3, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV000397737.9

Allele description [Variation Report for NM_001199397.3(NEK1):c.3075C>T (p.Asn1025=)]

NM_001199397.3(NEK1):c.3075C>T (p.Asn1025=)

Gene:
NEK1:NIMA related kinase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
4q33
Genomic location:
Preferred name:
NM_001199397.3(NEK1):c.3075C>T (p.Asn1025=)
HGVS:
  • NC_000004.12:g.169424700G>A
  • NG_027982.1:g.192928C>T
  • NM_001199397.3:c.3075C>TMANE SELECT
  • NM_001199398.3:c.2943C>T
  • NM_001199399.3:c.2784C>T
  • NM_001199400.3:c.2859C>T
  • NM_001374418.1:c.3075C>T
  • NM_001374419.1:c.2991C>T
  • NM_001374420.1:c.2940C>T
  • NM_001374421.1:c.2592C>T
  • NM_012224.4:c.2991C>T
  • NP_001186326.1:p.Asn1025=
  • NP_001186327.1:p.Asn981=
  • NP_001186328.1:p.Asn928=
  • NP_001186329.1:p.Asn953=
  • NP_001361347.1:p.Asn1025=
  • NP_001361348.1:p.Asn997=
  • NP_001361349.1:p.Asn980=
  • NP_001361350.1:p.Asn864=
  • NP_036356.1:p.Asn997=
  • NC_000004.11:g.170345851G>A
  • NM_012224.2:c.2991C>T
  • NR_164630.1:n.3537C>T
Links:
dbSNP: rs886059227
NCBI 1000 Genomes Browser:
rs886059227
Molecular consequence:
  • NR_164630.1:n.3537C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001199397.3:c.3075C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001199398.3:c.2943C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001199399.3:c.2784C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001199400.3:c.2859C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001374418.1:c.3075C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001374419.1:c.2991C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001374420.1:c.2940C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001374421.1:c.2592C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_012224.4:c.2991C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000448547Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Uncertain significance
(Jan 13, 2018) 		germlineclinical testing

Citation Link,

SCV004558664Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely benign
(Jan 3, 2024) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9..

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000448547.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004558664.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 16, 2025