CNMD

chondromodulin, the group of BRICHOS domain containing

Basic information

Region (hg38): 13:52703263-52739820

Previous symbols: [ "MYETS1", "LECT1" ]

Links

ENSG00000136110 ∙ NCBI:11061 ∙ OMIM:605147 ∙ HGNC:17005 ∙ Uniprot:O75829 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (5 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNMD 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					1	1
missense			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	1

Variants in CNMD

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

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

Position	Type	Phenotype	Significance	ClinVar
13-52703633-A-G		not specified	Uncertain significance (Jun 03, 2022)
13-52703656-G-A		not specified	Uncertain significance (Dec 01, 2022)
13-52703716-T-A		not specified	Uncertain significance (Oct 03, 2022)
13-52703719-T-G		not specified	Uncertain significance (Aug 01, 2022)
13-52703747-C-G		not specified	Uncertain significance (Sep 13, 2023)
13-52703759-T-G		not specified	Uncertain significance (May 04, 2023)
13-52703765-C-T		not specified	Uncertain significance (Nov 10, 2022)
13-52708549-T-A		not specified	Uncertain significance (Sep 22, 2023)
13-52712755-C-T		not specified	Uncertain significance (Sep 17, 2021)
13-52712866-C-T		not specified	Uncertain significance (Jan 30, 2024)
13-52724005-A-T		not specified	Uncertain significance (Aug 12, 2021)
13-52724019-T-C		not specified	Uncertain significance (Nov 09, 2021)
13-52724026-C-T		not specified	Likely benign (Oct 25, 2022)
13-52733293-C-T		not specified	Uncertain significance (May 16, 2023)
13-52733297-T-C		not specified	Uncertain significance (Dec 20, 2021)
13-52733328-T-C		not specified	Uncertain significance (Feb 06, 2023)
13-52739065-C-T		not specified	Uncertain significance (Oct 26, 2021)
13-52739109-C-A			Benign (Feb 22, 2018)
13-52739114-C-T		not specified	Uncertain significance (Jun 23, 2023)
13-52739640-C-A		not specified	Uncertain significance (Dec 14, 2023)
13-52739659-G-A		not specified	Uncertain significance (Nov 09, 2021)
13-52739664-A-C		not specified	Uncertain significance (Dec 13, 2023)
13-52739668-G-C		not specified	Uncertain significance (Aug 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNMD	protein_coding	protein_coding	ENST00000377962	7	36549

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000104	0.566	125525	2	221	125748	0.000887

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.400	171	186	0.918	0.00000971	2188
Missense in Polyphen		61	61.146	0.99761		677
Synonymous	-0.125	65	63.7	1.02	0.00000332	617
Loss of Function	0.902	11	14.7	0.746	6.26e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000799	0.000766
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000329	0.000277
European (Non-Finnish)	0.00126	0.00121
Middle Eastern	0.0000544	0.0000544
South Asian	0.00170	0.00167
Other	0.000824	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Bifunctional growth regulator that stimulates the growth of cultured chondrocytes in the presence of basic fibroblast growth factor (FGF) but inhibits the growth of cultured vascular endothelial cells. May contribute to the rapid growth of cartilage and vascular invasion prior to the replacement of cartilage by bone during endochondral bone development. Inhibits in vitro tube formation and mobilization of endothelial cells. Plays a role as antiangiogenic factor in cardiac valves to suppress neovascularization. {ECO:0000269|PubMed:16980969}.

Recessive Scores

• pRec: 0.152

Intolerance Scores

• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.82

Haploinsufficiency Scores

• pHI: 0.460
• hipred: N
• hipred_score: 0.300
• ghis: 0.518

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cnmd
• Phenotype: immune system phenotype; skeleton phenotype; hematopoietic system phenotype; normal phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: skeletal system development;endothelial cell morphogenesis;negative regulation of endothelial cell proliferation;proteoglycan metabolic process;negative regulation of angiogenesis;cell differentiation;negative regulation of vascular endothelial growth factor receptor signaling pathway;cartilage development
• Cellular component: extracellular region;endomembrane system;integral component of membrane