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NM_003193.5(TBCE):c.100+1G>A AND Autosomal recessive Kenny-Caffey syndrome

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Jan 15, 2020
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:
RCV001198592.5

Allele description [Variation Report for NM_003193.5(TBCE):c.100+1G>A]

NM_003193.5(TBCE):c.100+1G>A

Gene:
TBCE:tubulin folding cofactor E [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q42.3
Genomic location:
Preferred name:
NM_003193.5(TBCE):c.100+1G>A
HGVS:
  • NC_000001.11:g.235380150G>A
  • NG_009230.1:g.17738G>A
  • NG_009230.2:g.17725G>A
  • NM_001079515.3:c.100+1G>A
  • NM_001287801.2:c.100+1G>A
  • NM_001287802.2:c.-211+1G>A
  • NM_003193.5:c.100+1G>AMANE SELECT
  • NC_000001.10:g.235543465G>A
  • NM_001287801.1:c.100+1G>A
  • NM_003193.3:c.100+1G>A
  • NM_003193.4:c.100+1G>A
Links:
dbSNP: rs200356271
NCBI 1000 Genomes Browser:
rs200356271
Molecular consequence:
  • NM_001079515.3:c.100+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001287801.2:c.100+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001287802.2:c.-211+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_003193.5:c.100+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Autosomal recessive Kenny-Caffey syndrome (KCS1)
Synonyms:
Kenny-Caffey syndrome type 1
Identifiers:
MONDO: MONDO:0009486; MedGen: C1855648; Orphanet: 2333; OMIM: 244460

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001369582Centre for Mendelian Genomics, University Medical Centre Ljubljana
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Jan 15, 2020) 		unknownclinical testing

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

SCV004100908Department of Developmental Neurology, Medical University of Gdańsk
no classification provided
not providedunknownphenotyping only

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
Polishunknownyesnot providednot providednot providednot providednot providedphenotyping only

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001369582.2

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

Description

This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PM2.

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

From Department of Developmental Neurology, Medical University of Gdańsk, SCV004100908.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Polishnot providednot providednot providedphenotyping onlynot provided

Description

The variant substitutes a nucleotide within a canonical donor splice site and is therefore likely to lead to abnormal splicing.

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

Last Updated: Oct 8, 2024