COMMD9

COMM domain containing 9, the group of CCC complex|COMM domain containing

Basic information

Region (hg38): 11:36269284-36289449

Links

ENSG00000110442 ∙ NCBI:29099 ∙ OMIM:612299 ∙ HGNC:25014 ∙ Uniprot:Q9P000 ∙ 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 COMMD9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COMMD9 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	1

Variants in COMMD9

This is a list of pathogenic ClinVar variants found in the COMMD9 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-36274705-T-C		not specified	Uncertain significance (May 10, 2022)
11-36276168-A-G		not specified	Uncertain significance (Sep 06, 2022)
11-36276171-C-T		not specified	Uncertain significance (Apr 24, 2023)
11-36276223-C-T		not specified	Uncertain significance (Aug 02, 2021)
11-36276229-G-A		not specified	Uncertain significance (May 26, 2023)
11-36277119-T-C		not specified	Likely benign (Aug 11, 2022)
11-36278557-G-A			Benign (Dec 20, 2017)
11-36278574-G-A		not specified	Uncertain significance (Jun 24, 2022)
11-36278592-T-C		not specified	Uncertain significance (Jan 08, 2024)
11-36280717-C-G		not specified	Uncertain significance (Sep 25, 2023)
11-36280753-T-A		not specified	Uncertain significance (Jan 18, 2022)
11-36289390-T-A		not specified	Uncertain significance (Nov 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COMMD9	protein_coding	protein_coding	ENST00000263401	6	15949

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.394	0.598	125704	0	40	125744	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.479	97	111	0.872	0.00000628	1270
Missense in Polyphen		38	37.561	1.0117		450
Synonymous	-0.244	48	45.9	1.05	0.00000253	410
Loss of Function	2.21	2	9.25	0.216	3.91e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000499	0.000499
Ashkenazi Jewish	0.000704	0.000695
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.00	0.00
South Asian	0.000105	0.0000980
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May modulate activity of cullin-RING E3 ubiquitin ligase (CRL) complexes (PubMed:21778237). May down-regulate activation of NF-kappa-B (PubMed:15799966). Modulates Na(+) transport in epithelial cells by regulation of apical cell surface expression of amiloride-sensitive sodium channel (ENaC) subunits (PubMed:23637203). {ECO:0000269|PubMed:15799966, ECO:0000269|PubMed:23637203, ECO:0000305|PubMed:21778237}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Neutrophil degranulation;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Neddylation (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.32

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.333
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.159

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Commd9
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism 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); embryo phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: sodium ion transport;cholesterol homeostasis;neutrophil degranulation
• Cellular component: extracellular region;nucleus;Golgi apparatus;cytosol;secretory granule lumen;ficolin-1-rich granule lumen
• Molecular function: protein binding