NM_019026.6(TMCO1):c.323+3G>C AND Craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 15, 2014
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:: RCV000203247.1

Allele description [Variation Report for NM_019026.6(TMCO1):c.323+3G>C]

NM_019026.6(TMCO1):c.323+3G>C

Gene:

TMCO1:transmembrane and coiled-coil domains 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q24.1

Genomic location:

Preferred name:

NM_019026.6(TMCO1):c.323+3G>C

HGVS:

NC_000001.11:g.165752099C>G
NG_032004.1:g.21824G>C
NM_001256164.1:c.374+3G>C
NM_001256165.1:c.287+3G>C
NM_019026.6:c.323+3G>CMANE SELECT
NC_000001.10:g.165721336C>G
NM_019026.4:c.323G>C

Links:

dbSNP: rs372701032

NCBI 1000 Genomes Browser:

rs372701032

Molecular consequence:

NM_001256164.1:c.374+3G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001256165.1:c.287+3G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_019026.6:c.323+3G>C - intron variant - [Sequence Ontology: SO:0001627]

Functional consequence:

Variation affecting splicing function of RNA [Variation Ontology: 0397]
exon loss [Variation Ontology: 0381]

Condition(s)

Name:: Craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development 1 (CFSMR1)
Synonyms:: Cerebrofaciothoracic dysplasia; Craniofacial dysmorphism, skeletal anomalies, and mental retardation syndrome
Identifiers:: MONDO: MONDO:0800436; MedGen: C5677021; Orphanet: 1394; OMIM: 213980

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000256748	Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine	criteria provided, single submitter (Pehlivan_EJHG_2014_TMCO1)	Pathogenic (Jan 15, 2014)	inherited	research	PubMed (3) [See all records that cite these PMIDs] 23806086, 24088041, 24424126

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000256748

Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine

criteria provided, single submitter

(Pehlivan_EJHG_2014_TMCO1)

Pathogenic
(Jan 15, 2014)

inherited

research

PubMed (3)
[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	inherited	no	2	not provided	not provided	not provided	no	research
not provided	inherited	yes	1	1	not provided	not provided	no	research

Citations

PubMed

Exome sequencing resolves apparent incidental findings and reveals further complexity of SH3TC2 variant alleles causing Charcot-Marie-Tooth neuropathy.

Lupski JR, Gonzaga-Jauregui C, Yang Y, Bainbridge MN, Jhangiani S, Buhay CJ, Kovar CL, Wang M, Hawes AC, Reid JG, Eng C, Muzny DM, Gibbs RA.

Genome Med. 2013;5(6):57. doi: 10.1186/gm461.

PubMed [citation]

PMID:: 23806086
PMCID:: PMC3706849

Clinical whole-exome sequencing for the diagnosis of mendelian disorders.

Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, Braxton A, Beuten J, Xia F, Niu Z, Hardison M, Person R, Bekheirnia MR, Leduc MS, Kirby A, Pham P, Scull J, Wang M, Ding Y, Plon SE, Lupski JR, Beaudet AL, et al.

N Engl J Med. 2013 Oct 17;369(16):1502-11. doi: 10.1056/NEJMoa1306555. Epub 2013 Oct 2.

PubMed [citation]

PMID:: 24088041
PMCID:: PMC4211433

See all PubMed Citations (3)

PMC

Whole-exome sequencing links TMCO1 defect syndrome with cerebro-facio-thoracic dysplasia.

Pehlivan D, Karaca E, Aydin H, Beck CR, Gambin T, Muzny DM, Bilge Geckinli B, Karaman A, Jhangiani SN, Centers for Mendelian Genomics, Gibbs RA, Lupski JR.

European Journal of Human Genetics. 2014 Jan 15; 22(9): 1145-1148

PMC [article]

PMCID:: PMC4135405
PMID:: 24424126
DOI:: 10.1038/ejhg.2013.291

Details of each submission

From Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine, SCV000256748.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	no	research	PubMed (3)
2	not provided	2	not provided	no	research	PubMed (3)

Description

Homozygous variant in a Turkish individual; RNA demonstrates missplicing due to intronic variant (Skipping of exon 5)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	inherited	yes	not provided	Blood	not provided		1	not provided	1	not provided
2	inherited	no	not provided	Blood	not provided		2	not provided	not provided	not provided

Last Updated: Aug 5, 2023

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