C1QL3

protein-coding

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

Gene summary

Predicted to enable identical protein binding activity. Predicted to be involved in maintenance of synapse structure and trans-synaptic signaling, modulating synaptic transmission. Predicted to act upstream of or within regulation of synapse organization. Predicted to be located in extracellular region. Predicted to be active in obsolete extracellular space; synapse; and synaptic cleft. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001010908.2

Inheritance

—

ClinVar variants

U:33B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr10:16,513,734-16,521,879

External References & Databases

Ensembl (ENSG00000165985)

Transcript & Mutation Effects

hg38 • Region Span ~8.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to C1QL3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 29

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001010908.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar		1 clinvar	3
missense			31 clinvar			31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	33	0	1	34

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001010908.2	RefSeq	NP_001010908.1	2	MANE Select
ENST00000298943.4	Ensembl	ENSP00000298943.3	2	MANE Select
ENST00000718439.1	Ensembl	ENSP00000520824.1	2	Standard
ENST00000718439.2	Ensembl	ENSP00000520824.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of synapse organization

Molecular Function

identical protein binding

Cellular Component

extracellular region
collagen trimer

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000298943
Coding exons: 2
Length: 8263
Individuals with no LoFs: 125743
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125745
p: 0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.12	65	134	0.485	0.00000644	1626
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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