NM_003193.5(TBCE):c.155_166del (p.Ser52_Gly55del) AND Autosomal recessive Kenny-Caffey syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 1, 2002
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:: RCV000191990.7

Allele description [Variation Report for NM_003193.5(TBCE):c.155_166del (p.Ser52_Gly55del)]

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

Gene:

TBCE:tubulin folding cofactor E [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1q42.3

Genomic location:

Preferred name:

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

HGVS:

NC_000001.11:g.235401557_235401568del
NG_009230.1:g.39145_39156del
NM_001079515.3:c.155_166del
NM_001287801.2:c.155_166del
NM_001287802.2:c.-210-12876_-210-12865del
NM_003193.5:c.155_166delMANE SELECT
NP_001072983.1:p.Ser52_Gly55del
NP_001274730.1:p.Ser52_Gly55del
NP_003184.1:p.Ser52_Gly55del
NC_000001.10:g.235564868_235564879del
NC_000001.10:g.235564872_235564883del
NM_001079515.2:c.155_166delGCCACGAAGGGA
NM_001079515.3:c.155_166del
NM_001287801.1:c.155_166del
NM_003193.3:c.155_166del
NM_003193.4:c.155_166del
NM_003193.4:c.155_166delGCCACGAAGGGA

Note:

NCBI staff reviewed the sequence information reported in PubMed 12389028 Fig. 2a to determine the location of this allele on the current reference sequence.

Links:

OMIM: 604934.0001; dbSNP: rs767004810

NCBI 1000 Genomes Browser:

rs767004810

Molecular consequence:

NM_001079515.3:c.155_166del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001287801.2:c.155_166del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_003193.5:c.155_166del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001287802.2:c.-210-12876_-210-12865del - intron variant - [Sequence Ontology: SO:0001627]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000246253	OMIM	no assertion criteria provided	Pathogenic (Nov 1, 2002)	germline	literature only	PubMed (2) [See all records that cite these PMIDs] 12389028, 26336027

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000246253

OMIM

no assertion criteria provided

Pathogenic
(Nov 1, 2002)

germline

literature only

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Mutation of TBCE causes hypoparathyroidism-retardation-dysmorphism and autosomal recessive Kenny-Caffey syndrome.

Parvari R, Hershkovitz E, Grossman N, Gorodischer R, Loeys B, Zecic A, Mortier G, Gregory S, Sharony R, Kambouris M, Sakati N, Meyer BF, Al Aqeel AI, Al Humaidan AK, Al Zanhrani F, Al Swaid A, Al Othman J, Diaz GA, Weiner R, Khan KT, Gordon R, Gelb BD; et al.

Nat Genet. 2002 Nov;32(3):448-52. Epub 2002 Oct 21.

PubMed [citation]

PMID:: 12389028

The Bedouin mutation c.155-166del of the TBCE gene in a patient with Sanjad-Sakati syndrome of Moroccan origin.

Ratbi I, Lyahyai J, Kabiri M, Banouar M, Zerkaoui M, Barkat A, Sefiania A.

Ann Saudi Med. 2015 Mar-Apr;35(2):170-2. doi: 10.5144/0256-4947.2015.170.

PubMed [citation]

PMID:: 26336027
PMCID:: PMC6074128

Details of each submission

From OMIM, SCV000246253.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (2)

Description

Parvari et al. (2002) demonstrated homozygosity for a 12-bp deletion in the second coding exon of the TBCE gene in all Middle Eastern individuals with hypoparathyroidism-retardation-dysmorphism syndrome (HRDS; 241410) whom they evaluated (more than 50). The deletion was not present in more than 350 control chromosomes from Arab individuals.

All the Middle Eastern subjects studied by Parvari et al. (2002) had the 12-bp deletion in the TBCE gene; however, the phenotype in 8 pedigrees with 13 affected individuals was that of autosomal recessive Kenny-Caffey syndrome (KCS1; 244460), differing from the phenotype in HRDS families (17 Saudi pedigrees, 27 affected individuals; 9 Israeli pedigrees, 25 affected individuals) owing to the additional presence of medullary stenosis of the long bones, calvarial osteosclerosis, and susceptibility to bacterial infection. The presence of patchy osteosclerosis in the long bones of some Saudi patients with HRDS and deaths secondary to sepsis in some Israeli Bedouin individuals with HRDS suggested variable expression of these phenotypic features in a pedigree-specific fashion.

In a female infant, born of consanguineous Moroccan parents, with HRDS, Ratbi et al. (2015) identified homozygosity for the 12-bp deletion (c.155_166del12) that was previously found only in patients of Middle Eastern descent. The findings were consistent with the history of Arab migration to Morocco with the expansion of Islam to North Africa in the 7th century.

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

Last Updated: Oct 8, 2024

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