NM_001199397.3(NEK1):c.213del (p.Glu72fs) AND Short-rib thoracic dysplasia 6 with or without polydactyly

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 30, 2022
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:: RCV001822975.2

Allele description [Variation Report for NM_001199397.3(NEK1):c.213del (p.Glu72fs)]

NM_001199397.3(NEK1):c.213del (p.Glu72fs)

Gene:

NEK1:NIMA related kinase 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

4q33

Genomic location:

Preferred name:

NM_001199397.3(NEK1):c.213del (p.Glu72fs)

HGVS:

NC_000004.12:g.169602010del
NG_027982.1:g.15619del
NM_001199397.3:c.213delMANE SELECT
NM_001199398.3:c.213del
NM_001199399.3:c.213del
NM_001199400.3:c.213del
NM_001374418.1:c.213del
NM_001374419.1:c.213del
NM_001374420.1:c.213del
NM_001374421.1:c.213del
NM_001374422.1:c.213del
NM_001374423.1:c.213del
NM_012224.4:c.213del
NP_001186326.1:p.Glu72fs
NP_001186327.1:p.Glu72fs
NP_001186328.1:p.Glu72fs
NP_001186329.1:p.Glu72fs
NP_001361347.1:p.Glu72fs
NP_001361348.1:p.Glu72fs
NP_001361349.1:p.Glu72fs
NP_001361350.1:p.Glu72fs
NP_001361351.1:p.Glu72fs
NP_001361352.1:p.Glu72fs
NP_036356.1:p.Glu72fs
NC_000004.11:g.170523161del
NM_001199397.3:c.213delAMANE SELECT
NR_164630.1:n.825del
NR_164631.1:n.747del

Protein change:

E72fs

Links:

dbSNP: rs2150139071

NCBI 1000 Genomes Browser:

rs2150139071

Molecular consequence:

NM_001199397.3:c.213del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001199398.3:c.213del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001199399.3:c.213del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001199400.3:c.213del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374418.1:c.213del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374419.1:c.213del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374420.1:c.213del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374421.1:c.213del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374422.1:c.213del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374423.1:c.213del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_012224.4:c.213del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_164630.1:n.825del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164631.1:n.747del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002072468	Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital	no assertion criteria provided	Pathogenic (Jan 30, 2022)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002072468

Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital

no assertion criteria provided

Pathogenic
(Jan 30, 2022)

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
South East Asian	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, SCV002072468.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	South East Asian	1	not provided	not provided	clinical testing	not provided

Description

The homozygous frameshift deletion variant c.213delA (p.E72Kfs*6) has not been observed in gnomAD and 1000g. In-silico bioinformatic software predict this variant by mutation taster as Disease causing. The phenotype observed was short long bones, narrow thorax, horseshoe shaped kidneys, cleft lip and cleft palate. Short rib thoracic dysplasia 6 is an autosomal recessive disorder. Based on the phenotypic observation, we classify this variant as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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