CCM2L

CCM2 like scaffold protein

Basic information

Region (hg38): 20:32010437-32032180

Previous symbols: [ "C20orf160" ]

Links

ENSG00000101331 ∙ NCBI:140706 ∙ ∙ HGNC:16153 ∙ Uniprot:Q9NUG4 ∙ 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 CCM2L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCM2L 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						0
missense			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	0	0

Variants in CCM2L

This is a list of pathogenic ClinVar variants found in the CCM2L region.

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

Position	Type	Phenotype	Significance	ClinVar
20-32014946-G-A		not specified	Uncertain significance (Mar 18, 2024)
20-32014952-C-T		not specified	Uncertain significance (Oct 11, 2023)
20-32014979-C-T		not specified	Uncertain significance (Apr 20, 2023)
20-32014983-G-A		not specified	Uncertain significance (Feb 13, 2024)
20-32017806-G-A		not specified	Uncertain significance (May 17, 2023)
20-32017819-G-C		not specified	Uncertain significance (May 06, 2022)
20-32018060-T-G		not specified	Uncertain significance (Dec 21, 2023)
20-32018092-C-G		not specified	Uncertain significance (Mar 24, 2023)
20-32018949-G-A		not specified	Uncertain significance (Dec 01, 2022)
20-32019002-G-T		not specified	Uncertain significance (Mar 20, 2023)
20-32019006-C-A		not specified	Uncertain significance (Mar 15, 2024)
20-32019024-C-A		not specified	Uncertain significance (Aug 02, 2023)
20-32019047-A-C		not specified	Uncertain significance (Aug 04, 2021)
20-32019048-C-T		not specified	Uncertain significance (Nov 20, 2023)
20-32019059-C-T		not specified	Uncertain significance (Jan 03, 2022)
20-32019087-G-A		not specified	Uncertain significance (Feb 27, 2023)
20-32019090-T-G		not specified	Uncertain significance (Nov 08, 2021)
20-32019095-T-G		not specified	Uncertain significance (Aug 10, 2021)
20-32019096-G-C		not specified	Uncertain significance (Aug 02, 2023)
20-32019105-G-A		not specified	Uncertain significance (Dec 16, 2023)
20-32019117-C-G		not specified	Uncertain significance (Apr 09, 2024)
20-32019179-G-A		not specified	Uncertain significance (Nov 09, 2023)
20-32019207-G-A		not specified	Uncertain significance (Jun 17, 2024)
20-32019275-T-C		not specified	Uncertain significance (Jun 16, 2023)
20-32019320-C-T		not specified	Uncertain significance (Apr 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCM2L	protein_coding	protein_coding	ENST00000262659	8	21740

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.78e-7	0.743	125696	0	52	125748	0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.910	151	186	0.812	0.0000105	2722
Missense in Polyphen		58	77.761	0.74587		996
Synonymous	0.690	69	76.7	0.900	0.00000426	927
Loss of Function	1.25	12	17.6	0.680	9.14e-7	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000838	0.000831
Ashkenazi Jewish	0.000202	0.000198
East Asian	0.000183	0.000163
Finnish	0.000278	0.000277
European (Non-Finnish)	0.0000978	0.0000967
Middle Eastern	0.000183	0.000163
South Asian	0.0000338	0.0000327
Other	0.000492	0.000489

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.743
• hipred: N
• hipred_score: 0.364
• ghis: 0.607

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccm2l
• Phenotype: neoplasm; normal 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); cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype

Zebrafish Information Network

• Gene name: ccm2l
• Affected structure: subintestinal vein
• Phenotype tag: abnormal
• Phenotype quality: disheveled

Gene ontology

• Biological process: cardiac atrium morphogenesis;ventricular trabecula myocardium morphogenesis;biological_process;negative regulation of protein binding;negative regulation of homotypic cell-cell adhesion;wound healing;cardiac muscle tissue growth;positive regulation of fibroblast growth factor production
• Cellular component: cellular_component
• Molecular function: molecular_function