CLMP

CXADR like membrane protein, the group of IgCAM CXADR-related subfamily|I-set domain containing

Basic information

Region (hg38): 11:123069871-123195248

Links

ENSG00000166250 ∙ NCBI:79827 ∙ OMIM:611693 ∙ HGNC:24039 ∙ Uniprot:Q9H6B4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital short bowel syndrome, autosomal recessive (Strong), mode of inheritance: AR
• congenital short bowel syndrome, autosomal recessive (Moderate), mode of inheritance: AR
• congenital short bowel syndrome (Supportive), mode of inheritance: AR
• congenital short bowel syndrome, autosomal recessive (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital short bowel syndrome	AR	Gastrointestinal	Individuals have been described as benefiting from early introduction of enteral feeds, with later weaning from parenteral nutrition; Awareness of the risk of other GI-related complications may allow prompt recognition and management	Gastrointestinal	2005514; 10532268; 16707984; 18209785; 22155368

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLMP gene.

• Inborn genetic diseases (13 variants)
• not provided (8 variants)
• Congenital short bowel syndrome, autosomal recessive (4 variants)
• - (2 variants)
• Intestinal pseudo-obstruction (2 variants)
• Congenital short bowel syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLMP gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	4	6
missense			13		1	14
nonsense	2	2				4
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region						0
non coding						0
Total	2	3	13	2	5

Variants in CLMP

This is a list of pathogenic ClinVar variants found in the CLMP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-123073481-G-A		Inborn genetic diseases	Uncertain significance (Aug 15, 2023)
11-123073564-T-C			Likely benign (Dec 31, 2019)
11-123073585-C-T			Benign (Dec 31, 2019)
11-123073633-G-A		CLMP-related disorder	Likely benign (Jun 05, 2019)
11-123073649-C-T		Inborn genetic diseases	Uncertain significance (Jun 22, 2023)
11-123073704-G-A		Inborn genetic diseases	Uncertain significance (Nov 13, 2023)
11-123073708-G-A			Benign (Dec 31, 2019)
11-123073713-G-A		Inborn genetic diseases	Uncertain significance (Dec 06, 2021)
11-123073730-G-A		Inborn genetic diseases	Uncertain significance (Aug 10, 2023)
11-123073748-C-T		Inborn genetic diseases	Uncertain significance (Jul 26, 2022)
11-123074702-C-T		Congenital short bowel syndrome, autosomal recessive	Pathogenic (Mar 01, 2012)
11-123074795-G-A		Inborn genetic diseases	Uncertain significance (Feb 01, 2023)
11-123083097-C-G		Inborn genetic diseases	Uncertain significance (May 24, 2023)
11-123083100-G-A		Intestinal pseudo-obstruction • Congenital short bowel syndrome, autosomal recessive	Pathogenic (Dec 03, 2017)
11-123083142-A-G		Inborn genetic diseases	Uncertain significance (Oct 14, 2021)
11-123083180-A-T		Inborn genetic diseases	Uncertain significance (Sep 01, 2021)
11-123083190-G-A		Congenital short bowel syndrome, autosomal recessive	Likely pathogenic (-)
11-123083728-G-A		Intestinal pseudo-obstruction • Congenital short bowel syndrome • Congenital short bowel syndrome, autosomal recessive	Pathogenic/Likely pathogenic (Jan 25, 2023)
11-123083783-C-T		CLMP-related disorder	Benign (Dec 31, 2019)
11-123083815-C-A			Pathogenic (Nov 19, 2017)
11-123083826-C-T		-	no classification for the single variant (-)
11-123083828-C-T		CLMP-related disorder	Benign/Likely benign (Apr 12, 2019)
11-123084529-A-T		Congenital short bowel syndrome, autosomal recessive	Pathogenic (Mar 01, 2012)
11-123084547-C-T		Inborn genetic diseases	Uncertain significance (Apr 25, 2022)
11-123084563-C-T		Inborn genetic diseases	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLMP	protein_coding	protein_coding	ENST00000448775	7	122955

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.57e-7	0.853	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.583	183	207	0.886	0.0000112	2359
Missense in Polyphen		68	69.432	0.97937		825
Synonymous	0.216	76	78.4	0.969	0.00000390	782
Loss of Function	1.55	14	21.8	0.642	0.00000144	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000121	0.000120
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000153	0.000149
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the cell-cell adhesion. May play a role in adipocyte differentiation and development of obesity. Is required for normal small intestine development. {ECO:0000269|PubMed:14573622, ECO:0000269|PubMed:15563274, ECO:0000269|PubMed:22155368}.
• Disease: DISEASE: Congenital short bowel syndrome (CSBS) [MIM:615237]: A disease characterized by a shortened small intestine, intestinal malrotation, and malabsorption. The mean length of the small intestine in CSBS patients is approximately 50 cm, compared with a normal length at birth of 190-280 cm. Patients with CSBS may develop severe malnutrition as a result of the hugely reduced absorptive surface of the small intestine. Infants require parenteral nutrition for survival. However, parenteral nutrition itself causes life-threatening complications such as sepsis and liver failure which are associated with a high rate of mortality early in life. {ECO:0000269|PubMed:22155368}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.425
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Clmp
• Phenotype: digestive/alimentary phenotype; renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region phenotype; muscle phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: clmpa
• Affected structure: intestine
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: digestive tract development
• Cellular component: cytoplasmic microtubule;plasma membrane;bicellular tight junction;cell surface;integral component of membrane