C1QL3

complement C1q like 3, the group of C1q and TNF related

Basic information

Region (hg38): 10:16513734-16521879

Links

ENSG00000165985 ∙ NCBI:389941 ∙ OMIM:615227 ∙ HGNC:19359 ∙ Uniprot:Q5VWW1 ∙ 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 C1QL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1QL3 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	1

Variants in C1QL3

This is a list of pathogenic ClinVar variants found in the C1QL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-16514613-T-C		not specified	Uncertain significance (Apr 01, 2024)
10-16514628-G-A		not specified	Uncertain significance (Jul 27, 2024)
10-16520537-C-T		not specified	Uncertain significance (Sep 01, 2021)
10-16520610-G-A			Benign (Jun 12, 2018)
10-16520693-G-A		not specified	Uncertain significance (Aug 05, 2024)
10-16520726-C-G		not specified	Uncertain significance (May 23, 2024)
10-16520773-C-G		not specified	Uncertain significance (Nov 15, 2024)
10-16520785-C-T		not specified	Uncertain significance (Jun 27, 2023)
10-16520786-C-G		not specified	Uncertain significance (May 31, 2022)
10-16520792-C-G		not specified	Uncertain significance (Jun 30, 2024)
10-16520924-C-G		not specified	Uncertain significance (Dec 04, 2023)
10-16520947-G-A		not specified	Uncertain significance (Nov 17, 2022)
10-16520999-C-T		not specified	Uncertain significance (May 01, 2022)
10-16521005-G-A		not specified	Uncertain significance (Nov 26, 2024)
10-16521047-T-C		not specified	Uncertain significance (Mar 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1QL3	protein_coding	protein_coding	ENST00000298943	2	8263

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.516	0.469	125743	0	2	125745	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.12	65	134	0.485	0.00000644	1626
Missense in Polyphen		15	45.007	0.33328		497
Synonymous	0.691	52	58.7	0.885	0.00000310	524
Loss of Function	1.94	1	6.22	0.161	2.65e-7	78

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000126	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate the number of excitatory synapses that are formed on hippocampus neurons. Has no effect on inhibitory synapses (By similarity). Plays a role in glucose homeostasis. Via AMPK signaling pathway, stimulates glucose uptake in adipocytes, myotubes and hepatocytes and enhances insulin-stimulated glucose uptake. In a hepatoma cell line, reduces the expression of gluconeogenic enzymes G6PC and PCK1 and hence decreases de novo glucose production (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.124

Haploinsufficiency Scores

• pHI: 0.581
• hipred: Y
• hipred_score: 0.736
• ghis: 0.618

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: C1ql3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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: regulation of synapse organization
• Cellular component: extracellular region;collagen trimer
• Molecular function: identical protein binding