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NM_003193.5(TBCE):c.155_166del (p.Ser52_Gly55del)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Sep 1, 2021)
Last evaluated:
Jan 29, 2020
Accession:
VCV000005290.6
Variation ID:
5290
Description:
12bp deletion
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NM_003193.5(TBCE):c.155_166del (p.Ser52_Gly55del)

Allele ID
20329
Variant type
Deletion
Variant length
12 bp
Cytogenetic location
1q42.3
Genomic location
1: 235401553-235401564 (GRCh38) GRCh38 UCSC
1: 235564868-235564879 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_003193.4:c.155_166delGCCACGAAGGGA
NC_000001.10:g.235564872_235564883del
NC_000001.11:g.235401557_235401568del
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:235401552:GGGAGCCACGAAGGGA:GGGA
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA212825
OMIM: 604934.0001
dbSNP: rs767004810
VarSome
Comment on variant
NCBI staff reviewed the sequence information reported in PubMed 12389028 Fig. 2a to determine the location of this allele on the current reference sequence.
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 5 criteria provided, multiple submitters, no conflicts Mar 16, 2018 RCV000005608.6
Pathogenic 2 criteria provided, multiple submitters, no conflicts Jan 29, 2020 RCV000224858.4
Pathogenic 1 no assertion criteria provided Nov 1, 2002 RCV000191990.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
TBCE - - GRCh38
GRCh38
GRCh37
151 260

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Dec 18, 2014)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000280889.1
Submitted: (May 19, 2016)
Evidence details
Likely pathogenic
(Mar 16, 2018)
criteria provided, single submitter
Method: clinical testing
Hypoparathyroidism-retardation-dysmorphism syndrome
Allele origin: inherited
Centre for Translational Omics - GOSgene,University College London
Accession: SCV000778576.1
Submitted: (Jun 12, 2018)
Evidence details
Pathogenic
(Dec 30, 2017)
criteria provided, single submitter
Method: clinical testing
Hypoparathyroidism-retardation-dysmorphism syndrome
Allele origin: unknown
Department of Genetics,Sultan Qaboos University Hospital, Oman
Accession: SCV000891681.1
Submitted: (Oct 25, 2018)
Evidence details
Publications
PubMed (1)
Pathogenic
(-)
criteria provided, single submitter
Method: clinical testing
Hypoparathyroidism-retardation-dysmorphism syndrome
Allele origin: germline
Pathology and Clinical Laboratory Medicine,King Fahad Medical City
Accession: SCV000996294.1
Submitted: (Jun 18, 2019)
Evidence details
Pathogenic
(Jan 29, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001820079.1
Submitted: (Sep 01, 2021)
Evidence details
Comment:
In-frame deletion of 4 amino acids in a non-repeat region; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This … (more)
Pathogenic
(Nov 01, 2002)
no assertion criteria provided
Method: literature only
HYPOPARATHYROIDISM-RETARDATION-DYSMORPHISM SYNDROME
Allele origin: germline
OMIM
Accession: SCV000025790.3
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (2)
Pathogenic
(Nov 01, 2002)
no assertion criteria provided
Method: literature only
KENNY-CAFFEY SYNDROME, TYPE 1
Allele origin: germline
OMIM
Accession: SCV000246253.2
Submitted: (Sep 28, 2015)
Evidence details
Publications
PubMed (2)
Pathogenic
(Feb 05, 2020)
no assertion criteria provided
Method: clinical testing
Hypoparathyroidism-retardation-dysmorphism syndrome
Allele origin: germline
Biochemical Molecular Genetic Laboratory,King Abdulaziz Medical City
Accession: SCV001190740.1
Submitted: (Feb 12, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
The Bedouin mutation c.155-166del of the TBCE gene in a patient with Sanjad-Sakati syndrome of Moroccan origin. Ratbi I Annals of Saudi medicine 2015 PMID: 26336027
New Ocular Associations in Sanjad-Sakati Syndrome: Case report from Oman. Haider AS Sultan Qaboos University medical journal 2014 PMID: 25097779
Mutation of TBCE causes hypoparathyroidism-retardation-dysmorphism and autosomal recessive Kenny-Caffey syndrome. Parvari R Nature genetics 2002 PMID: 12389028

Text-mined citations for rs767004810...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 24, 2021