C1QTNF9B

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

Basic information

Region (hg38): 13:23891099-23897502

Links

ENSG00000205863 ∙ NCBI:387911 ∙ OMIM:614148 ∙ HGNC:34072 ∙ Uniprot:B2RNN3 ∙ 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 C1QTNF9B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1QTNF9B 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	2
missense			31	3	2	36
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	4	3

Variants in C1QTNF9B

This is a list of pathogenic ClinVar variants found in the C1QTNF9B region.

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

Position	Type	Phenotype	Significance	ClinVar
13-23891312-A-G		not specified	Uncertain significance (Nov 08, 2024)
13-23891333-C-T		not specified	Uncertain significance (Jan 18, 2023)
13-23891334-G-A			Benign (Aug 02, 2017)
13-23891334-G-T		not specified	Uncertain significance (Mar 21, 2023)
13-23891350-A-G		not specified	Uncertain significance (Feb 15, 2023)
13-23891356-T-C		not specified	Uncertain significance (Dec 20, 2023)
13-23891362-C-T		not specified	Uncertain significance (May 21, 2024)
13-23891381-G-T		not specified	Uncertain significance (Oct 09, 2024)
13-23891387-A-C		not specified	Uncertain significance (Nov 01, 2022)
13-23891419-A-C		not specified	Uncertain significance (Mar 04, 2024)
13-23891423-T-C		not specified	Likely benign (Feb 15, 2023)
13-23891450-C-T		not specified	Likely benign (Nov 30, 2021)
13-23891461-C-T			Benign (Jul 20, 2018)
13-23891500-A-T		not specified	Uncertain significance (May 05, 2023)
13-23891545-T-C		not specified	Uncertain significance (Aug 10, 2021)
13-23891564-A-T			Benign (Jul 26, 2018)
13-23891702-G-C		not specified	Uncertain significance (Nov 28, 2023)
13-23891759-G-A		not specified	Uncertain significance (Oct 03, 2024)
13-23891780-G-T		not specified	Uncertain significance (Aug 20, 2024)
13-23891865-A-C		not specified	Uncertain significance (Nov 09, 2024)
13-23891944-C-T		not specified	Uncertain significance (Dec 22, 2023)
13-23894164-C-A			Likely benign (Jun 01, 2022)
13-23894199-C-T		not specified	Uncertain significance (Jan 04, 2022)
13-23896829-C-T		not specified	Uncertain significance (Apr 01, 2024)
13-23896833-T-G		not specified	Uncertain significance (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1QTNF9B	protein_coding	protein_coding	ENST00000382137	3	11557

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.25e-8	0.184	125523	7	218	125748	0.000895

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.181	176	183	0.962	0.00000945	2090
Missense in Polyphen		76	75.137	1.0115		848
Synonymous	-0.118	76	74.7	1.02	0.00000439	683
Loss of Function	0.231	12	12.9	0.931	8.93e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000754	0.000753
Ashkenazi Jewish	0.00491	0.00418
East Asian	0.00322	0.00321
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000390	0.000360
Middle Eastern	0.00322	0.00321
South Asian	0.00181	0.00170
Other	0.00122	0.00114

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.74

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.305
• ghis: 0.418

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

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

• Cellular component: extracellular region;collagen trimer
• Molecular function: protein binding