CD109

CD109 molecule, the group of CD molecules|C3 and PZP like, alpha-2-macroglobulin domain containing

Basic information

Region (hg38): 6:73695784-73828316

Links

ENSG00000156535 ∙ NCBI:135228 ∙ OMIM:608859 ∙ HGNC:21685 ∙ Uniprot:Q6YHK3 ∙ 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 CD109 gene.

• Inborn genetic diseases (61 variants)
• not provided (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD109 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	3	4
missense			57	8	4	69
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	4	5
non coding					2	2
Total	0	0	57	9	9

Variants in CD109

This is a list of pathogenic ClinVar variants found in the CD109 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-73696223-G-T		not specified	Uncertain significance (Jun 18, 2021)
6-73696285-C-T		not specified	Uncertain significance (Jun 30, 2022)
6-73697404-C-T		not specified	Uncertain significance (Jan 16, 2024)
6-73697425-G-A		not specified	Uncertain significance (Dec 21, 2022)
6-73697504-C-T		not specified	Uncertain significance (Nov 09, 2021)
6-73697534-C-G		not specified	Uncertain significance (Jan 09, 2024)
6-73730401-G-A		not specified	Uncertain significance (Jan 26, 2022)
6-73730412-A-T		not specified	Uncertain significance (Jun 23, 2023)
6-73730563-A-T		not specified	Uncertain significance (Feb 03, 2022)
6-73736473-A-G		not specified	Uncertain significance (Jul 30, 2023)
6-73736491-A-G			Benign (Nov 01, 2022)
6-73756680-A-G		not specified	Uncertain significance (Mar 22, 2023)
6-73758991-A-G		not specified	Uncertain significance (May 18, 2022)
6-73758995-A-G		not specified	Uncertain significance (Nov 09, 2022)
6-73759022-C-T		not specified	Uncertain significance (Feb 16, 2023)
6-73762742-T-C		not specified	Uncertain significance (Mar 22, 2023)
6-73762780-A-G		not specified	Uncertain significance (May 23, 2023)
6-73762838-C-G		not specified	Uncertain significance (Nov 18, 2022)
6-73763626-A-G		not specified	Uncertain significance (Jan 29, 2024)
6-73765952-G-A			Benign (Nov 01, 2022)
6-73765963-A-T		not specified	Uncertain significance (Sep 14, 2021)
6-73765967-T-C		not specified	Likely benign (Dec 07, 2021)
6-73766068-C-G			Likely benign (Jul 01, 2022)
6-73766070-G-C		not specified	Uncertain significance (Oct 25, 2023)
6-73766089-C-T		not specified	Uncertain significance (May 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD109	protein_coding	protein_coding	ENST00000287097	33	132533

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.27e-44	8.72e-7	125409	2	337	125748	0.00135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.503	755	717	1.05	0.0000342	9426
Missense in Polyphen		183	157.96	1.1585		2136
Synonymous	0.459	253	262	0.964	0.0000130	2749
Loss of Function	0.221	68	70.0	0.972	0.00000325	917

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00256	0.00256
Ashkenazi Jewish	0.000899	0.000893
East Asian	0.00188	0.00180
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00102	0.00101
Middle Eastern	0.00188	0.00180
South Asian	0.00359	0.00344
Other	0.000987	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Modulates negatively TGFB1 signaling in keratinocytes. {ECO:0000269|PubMed:16754747}.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 1.00
• rvis_EVS: 4.68
• rvis_percentile_EVS: 99.78

Haploinsufficiency Scores

• pHI: 0.269
• hipred: N
• hipred_score: 0.152
• ghis: 0.391

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.356

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd109
• Phenotype: endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: negative regulation of protein phosphorylation;hair follicle development;platelet degranulation;negative regulation of keratinocyte proliferation;negative regulation of endopeptidase activity;negative regulation of transforming growth factor beta receptor signaling pathway;regulation of keratinocyte differentiation;negative regulation of wound healing;osteoclast fusion
• Cellular component: extracellular region;extracellular space;plasma membrane;cell surface;platelet alpha granule membrane;anchored component of membrane
• Molecular function: serine-type endopeptidase inhibitor activity;transforming growth factor beta binding