NM_001371623.1(TCOF1):c.2575C>G (p.Gln859Glu) AND Treacher Collins syndrome 1

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Apr 26, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV000490303.3

Allele description [Variation Report for NM_001371623.1(TCOF1):c.2575C>G (p.Gln859Glu)]

NM_001371623.1(TCOF1):c.2575C>G (p.Gln859Glu)

Gene:

TCOF1:treacle ribosome biogenesis factor 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q32

Genomic location:

Preferred name:

NM_001371623.1(TCOF1):c.2575C>G (p.Gln859Glu)

HGVS:

NC_000005.10:g.150379325C>G
NG_011341.1:g.26687C>G
NM_000356.4:c.2344C>G
NM_001008657.3:c.2575C>G
NM_001135243.2:c.2575C>G
NM_001135244.2:c.2575C>G
NM_001135245.2:c.2344C>G
NM_001195141.2:c.2575C>G
NM_001371623.1:c.2575C>GMANE SELECT
NP_000347.2:p.Gln782Glu
NP_001008657.1:p.Gln859Glu
NP_001128715.1:p.Gln859Glu
NP_001128715.1:p.Gln859Glu
NP_001128716.1:p.Gln859Glu
NP_001128717.1:p.Gln782Glu
NP_001182070.1:p.Gln859Glu
NP_001358552.1:p.Gln859Glu
NC_000005.9:g.149758888C>G
NM_001135243.1:c.2575C>G

Protein change:

Q782E

Links:

dbSNP: rs201043592

NCBI 1000 Genomes Browser:

rs201043592

Molecular consequence:

NM_000356.4:c.2344C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001008657.3:c.2575C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001135243.2:c.2575C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001135244.2:c.2575C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001135245.2:c.2344C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001195141.2:c.2575C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001371623.1:c.2575C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000267521	Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 18, 2016)	germline	reference population	PubMed (2) [See all records that cite these PMIDs] 23967202, 25741868
SCV004284372	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Apr 26, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000267521

Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Mar 18, 2016)

germline

reference population

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

SCV004284372

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Apr 26, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
East Asian	germline	unknown	1	not provided	not provided	not provided	not provided	reference population

Citations

PubMed

Targeted exon sequencing successfully discovers rare causative genes and clarifies the molecular epidemiology of Japanese deafness patients.

Miyagawa M, Naito T, Nishio SY, Kamatani N, Usami S.

PLoS One. 2013;8(8):e71381. doi: 10.1371/journal.pone.0071381.

PubMed [citation]

PMID:: 23967202
PMCID:: PMC3742761

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

See all PubMed Citations (3)

Details of each submission

From Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center, SCV000267521.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	East Asian	1	not provided	not provided	reference population	PubMed (2)

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004284372.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

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

Last Updated: Sep 29, 2024

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