C1QTNF9

C1q and TNF related 9, the group of C1q and TNF related

Basic information

Region (hg38): 13:24307165-24322535

Links

ENSG00000240654 ∙ NCBI:338872 ∙ OMIM:614285 ∙ HGNC:28732 ∙ Uniprot:P0C862 ∙ 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 C1QTNF9 gene.

• Inborn genetic diseases (23 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1QTNF9 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			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in C1QTNF9

This is a list of pathogenic ClinVar variants found in the C1QTNF9 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-24316068-C-A		not specified	Uncertain significance (May 18, 2023)
13-24316111-C-G		not specified	Uncertain significance (Dec 20, 2021)
13-24316113-A-G		not specified	Uncertain significance (May 03, 2023)
13-24316114-T-A		not specified	Uncertain significance (Jul 09, 2021)
13-24316128-G-T		not specified	Uncertain significance (May 10, 2023)
13-24316142-G-A		not specified	Uncertain significance (Sep 14, 2022)
13-24316146-C-T		not specified	Uncertain significance (Aug 02, 2022)
13-24316163-G-A		not specified	Uncertain significance (Jan 31, 2023)
13-24321070-C-T		not specified	Uncertain significance (Dec 06, 2022)
13-24321154-G-A		not specified	Uncertain significance (Oct 24, 2023)
13-24321218-C-T		not specified	Uncertain significance (Aug 08, 2023)
13-24321272-C-T		not specified	Likely benign (Nov 29, 2021)
13-24321282-G-C		not specified	Uncertain significance (Jun 11, 2021)
13-24321298-C-T		not specified	Uncertain significance (Feb 14, 2023)
13-24321346-G-A		not specified	Uncertain significance (Apr 13, 2023)
13-24321356-T-C		not specified	Likely benign (May 31, 2023)
13-24321382-G-T		not specified	Uncertain significance (Aug 17, 2022)
13-24321454-G-A		not specified	Uncertain significance (Jul 06, 2021)
13-24321491-C-T		not specified	Uncertain significance (Sep 14, 2022)
13-24321496-C-T		not specified	Uncertain significance (Sep 28, 2022)
13-24321550-G-C		not specified	Uncertain significance (Dec 13, 2022)
13-24321634-G-A		not specified	Uncertain significance (Aug 13, 2021)
13-24321733-A-G		not specified	Uncertain significance (Dec 27, 2023)
13-24321757-A-G		not specified	Uncertain significance (Mar 11, 2022)
13-24321761-G-A		not specified	Uncertain significance (Dec 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1QTNF9	protein_coding	protein_coding	ENST00000382071	3	15370

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000114	0.603	125562	0	186	125748	0.000740

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.569	156	177	0.880	0.00000947	2105
Missense in Polyphen		68	85.083	0.79922		1004
Synonymous	0.453	67	71.9	0.932	0.00000431	690
Loss of Function	0.837	9	12.1	0.741	8.46e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000716	0.000702
Ashkenazi Jewish	0.00	0.00
East Asian	0.00778	0.00780
Finnish	0.00	0.00
European (Non-Finnish)	0.000174	0.000167
Middle Eastern	0.00778	0.00780
South Asian	0.000328	0.000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable adipokine. Activates AMPK, AKT, and p44/42 MAPK signaling pathways. {ECO:0000250|UniProtKB:Q4ZJN1}.

Recessive Scores

• pRec: 0.0880

Intolerance Scores

• loftool: 0.460
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.37

Haploinsufficiency Scores

• pHI: 0.0450
• hipred: N
• hipred_score: 0.249

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.145

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C1qtnf9
• Phenotype: homeostasis/metabolism phenotype; muscle phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype; liver/biliary system 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of signaling receptor activity
• Cellular component: extracellular region;collagen trimer
• Molecular function: hormone activity;protein binding;identical protein binding