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NM_001371623.1(TCOF1):c.3698_3702del (p.Ser1233fs) AND Treacher Collins syndrome 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 3, 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:
RCV001389715.2

Allele description

NM_001371623.1(TCOF1):c.3698_3702del (p.Ser1233fs)

Gene:
TCOF1:treacle ribosome biogenesis factor 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
5q32
Genomic location:
Preferred name:
NM_001371623.1(TCOF1):c.3698_3702del (p.Ser1233fs)
HGVS:
  • NC_000005.10:g.150393466_150393470del
  • NG_011341.1:g.40828_40832del
  • NM_000356.4:c.3464_3468del
  • NM_001135243.2:c.3695_3699del
  • NM_001135244.2:c.3584_3588del
  • NM_001135245.2:c.3467_3471del
  • NM_001195141.2:c.3581_3585del
  • NM_001371623.1:c.3698_3702delMANE SELECT
  • NP_000347.2:p.Ser1155fs
  • NP_001128715.1:p.Ser1232fs
  • NP_001128716.1:p.Ser1195fs
  • NP_001128717.1:p.Ser1156fs
  • NP_001182070.1:p.Ser1194fs
  • NP_001358552.1:p.Ser1233fs
  • NC_000005.9:g.149773028_149773032del
  • NC_000005.9:g.149773029_149773033del
Protein change:
S1155fs
Links:
dbSNP: rs2151060146
NCBI 1000 Genomes Browser:
rs2151060146
Molecular consequence:
  • NM_000356.4:c.3464_3468del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001135243.2:c.3695_3699del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001135244.2:c.3584_3588del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001135245.2:c.3467_3471del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001195141.2:c.3581_3585del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001371623.1:c.3698_3702del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Treacher Collins syndrome 1 (TCS1)
Identifiers:
MONDO: MONDO:0007944; MedGen: CN315775; Orphanet: 861; OMIM: 154500

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001591166Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jun 3, 2020) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Treacher Collins syndrome may result from insertions, deletions or splicing mutations, which introduce a termination codon into the gene.

Gladwin AJ, Dixon J, Loftus SK, Edwards S, Wasmuth JJ, Hennekam RC, Dixon MJ.

Hum Mol Genet. 1996 Oct;5(10):1533-8.

PubMed [citation]
PMID:
8894686

Gross deletions in TCOF1 are a cause of Treacher-Collins-Franceschetti syndrome.

Bowman M, Oldridge M, Archer C, O'Rourke A, McParland J, Brekelmans R, Seller A, Lester T.

Eur J Hum Genet. 2012 Jul;20(7):769-77. doi: 10.1038/ejhg.2012.2. Epub 2012 Feb 8.

PubMed [citation]
PMID:
22317976
PMCID:
PMC3376267
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001591166.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Ser1232Tyrfs*7) in the TCOF1 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with TCOF1-related conditions. Loss-of-function variants in TCOF1 are known to be pathogenic (PMID: 8894686, 22317976). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Dec 24, 2023