C1QTNF2

C1q and TNF related 2, the group of C1q and TNF related

Basic information

Region (hg38): 5:160347754-160370641

Links

ENSG00000145861 ∙ NCBI:114898 ∙ OMIM:618647 ∙ HGNC:14325 ∙ Uniprot:Q9BXJ5 ∙ 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 C1QTNF2 gene.

• not_specified (52 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1QTNF2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000031908.6. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			50	1		51
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	50	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1QTNF2	protein_coding	protein_coding	ENST00000393975	3	22891

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000835	0.799	125707	0	40	125747	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.182	206	199	1.04	0.0000129	2084
Missense in Polyphen		68	64.996	1.0462		658
Synonymous	-0.159	90	88.1	1.02	0.00000629	716
Loss of Function	1.09	6	9.65	0.622	5.13e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000310	0.000298
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000930	0.0000924
European (Non-Finnish)	0.000143	0.000141
Middle Eastern	0.00	0.00
South Asian	0.000397	0.000392
Other	0.000204	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.144

Intolerance Scores

• loftool: 0.289
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• pHI: 0.165
• hipred: N
• hipred_score: 0.282
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.102

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C1qtnf2
• Phenotype: skeleton phenotype

Gene ontology

• Biological process: activation of MAPK activity;positive regulation of glycogen biosynthetic process;positive regulation of fatty acid oxidation;positive regulation of glucose import;protein homooligomerization;protein heterotrimerization
• Cellular component: collagen trimer;extracellular space
• Molecular function: signaling receptor binding;protein binding;identical protein binding