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NM_174916.3(UBR1):c.4107T>A (p.Cys1369Ter) AND Johanson-Blizzard syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 30, 2014
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:
RCV000190636.4

Allele description [Variation Report for NM_174916.3(UBR1):c.4107T>A (p.Cys1369Ter)]

NM_174916.3(UBR1):c.4107T>A (p.Cys1369Ter)

Gene:
UBR1:ubiquitin protein ligase E3 component n-recognin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q15.2
Genomic location:
Preferred name:
NM_174916.3(UBR1):c.4107T>A (p.Cys1369Ter)
HGVS:
  • NC_000015.10:g.42983940A>T
  • NG_012182.1:g.127149T>A
  • NM_174916.3:c.4107T>AMANE SELECT
  • NP_777576.1:p.Cys1369Ter
  • NC_000015.9:g.43276138A>T
  • NM_174916.2:c.4107T>A
Protein change:
C1369*
Links:
dbSNP: rs797045112
NCBI 1000 Genomes Browser:
rs797045112
Molecular consequence:
  • NM_174916.3:c.4107T>A - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Name:
Johanson-Blizzard syndrome (JBS)
Synonyms:
Nasal alar hypoplasia, hypothyroidism, pancreatic achylia and congenital deafness
Identifiers:
MONDO: MONDO:0009479; MedGen: C0175692; Orphanet: 2315; OMIM: 243800

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000245679Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine - CSER-MedSeq
criteria provided, single submitter

(LMM Criteria)		Pathogenic
(Sep 30, 2014) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided11not providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine - CSER-MedSeq, SCV000245679.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The Cys1369X variant in UBR1 has not been previously reported in individuals with Johanson-Blizzard syndrome (JBS) or in large population studies. This nonsense variant leads to a premature termination codon at position 1369 which is predicted to lead to a truncated or absent protein. Complete loss of UBR1 function is an established disease mechanism in JBS (http://omim.org/entry/605981) .In summary, this variant meets our criteria to be classified as pathogenic for JBS in an autosomal recessive manner (http://personalizedmedicine.partners.org/Laboratory-For-Molecular-Medicine/).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided1not provided1not provided

Last Updated: Dec 24, 2022