NM_024769.4(CLMP):c.664C>T (p.Arg222Ter) AND Intestinal pseudo-obstruction

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Dec 3, 2017
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000043526.5

Allele description

NM_024769.4(CLMP):c.664C>T (p.Arg222Ter)

Gene:

CLMP:CXADR like membrane protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q24.1

Genomic location:

Preferred name:

NM_024769.4(CLMP):c.664C>T (p.Arg222Ter)

HGVS:

NC_000011.10:g.123083100G>A
NG_042818.1:g.117206C>T
NM_024769.4:c.664C>T
NP_079045.1:p.Arg222Ter
NP_079045.1:p.Arg222Ter
NP_079045.1:p.Arg222Ter
NC_000011.9:g.122953808G>A
NM_024769.2:c.664C>T
NM_024769.3:c.664C>T

Protein change:

R222*; ARG222TER

Links:

OMIM: 611693.0003; dbSNP: rs587776966

NCBI 1000 Genomes Browser:

rs587776966

Molecular consequence:

NM_024769.4:c.664C>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Name:: Intestinal pseudo-obstruction (CSBS)
Synonyms:: Congenital short bowel syndrome; Intestinal pseudoobstruction; Hollow visceral myopathy
Identifiers:: MedGen: C0021847; Orphanet: 2301; OMIM: 615237; Human Phenotype Ontology: HP:0004389

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000067395	OMIM	no assertion criteria provided	Pathogenic (Mar 1, 2012)	germline	literature only	PubMed (2) [See all records that cite these PMIDs] 18209785, 22155368 Hofstra, R. W. M. Personal Communication. 2013. Groningen, The Netherlands,
SCV000586796	Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement,Assistance Publique Hopitaux de Paris	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 6, 2017)	inherited	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 28708303
SCV000746333	Genomic Research Center, Shahid Beheshti University of Medical Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Dec 3, 2017)	inherited	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

SCV000067395

OMIM

no assertion criteria provided

Pathogenic
(Mar 1, 2012)

germline

literature only

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

Hofstra, R. W. M. Personal Communication. 2013. Groningen, The Netherlands,

SCV000586796

Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement,Assistance Publique Hopitaux de Paris

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 6, 2017)

inherited

clinical testing

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

SCV000746333

Genomic Research Center, Shahid Beheshti University of Medical Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Dec 3, 2017)

inherited

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	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	inherited	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Congenital short bowel syndrome: a case report and review of the literature.

Hasosah M, Lemberg DA, Skarsgard E, Schreiber R.

Can J Gastroenterol. 2008 Jan;22(1):71-4. Review.

PubMed [citation]

PMID:: 18209785
PMCID:: PMC2659124

CLMP is required for intestinal development, and loss-of-function mutations cause congenital short-bowel syndrome.

Van Der Werf CS, Wabbersen TD, Hsiao NH, Paredes J, Etchevers HC, Kroisel PM, Tibboel D, Babarit C, Schreiber RA, Hoffenberg EJ, Vekemans M, Zeder SL, Ceccherini I, Lyonnet S, Ribeiro AS, Seruca R, Te Meerman GJ, van Ijzendoorn SC, Shepherd IT, Verheij JB, Hofstra RM.

Gastroenterology. 2012 Mar;142(3):453-462.e3. doi: 10.1053/j.gastro.2011.11.038. Epub 2011 Dec 7.

PubMed [citation]

PMID:: 22155368

See all PubMed Citations (4)

Details of each submission

From OMIM, SCV000067395.5

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

Description

In a Canadian boy with congenital short bowel syndrome (CSBS; 615237) originally reported by Hasosah et al. (2008), van der Werf et al. (2012) identified homozygosity for a c.666C-T transition in exon 5 of the CLMP gene, resulting in an arg222-to-ter (R222X) substitution. The mutation was also found in homozygosity in an affected female relative and in heterozygosity in the unaffected parents, but it was not found in known SNP databases or in 154 Caucasian control chromosomes. The nucleotide numbering in the article by van der Werf et al. (2012) differed between the text and Table 1; the numbering cited here corresponds to that given in Table 1, which Hofstra (2013) confirmed was correct.

#	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

From Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement,Assistance Publique Hopitaux de Paris, SCV000586796.1

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

Description

neonatal feeding difficulties; no Intellectual disability

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

From Genomic Research Center, Shahid Beheshti University of Medical Sciences, SCV000746333.1

#	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	inherited	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 23, 2021

ClinVar

Relating variation to medicine