C1QL3

Chr 10

complement C1q like 3

Also known as: C1QTNF13, C1ql, CTRP13, K100

NCBI Gene: 389941ENSG00000165985UniProt: Q5VWW1

Predicted to enable identical protein binding activity. Predicted to be involved in neurotransmitter receptor localization to postsynaptic specialization membrane and postsynaptic density assembly. Predicted to act upstream of or within regulation of synapse organization. Predicted to be located in extracellular region. Predicted to be part of collagen trimer. Predicted to be active in glutamatergic synapse; hippocampal mossy fiber to CA3 synapse; and synaptic cleft. [provided by Alliance of Genome Resources, Jul 2025]

Research Assistant →
0
Active trials
5
Pubs (1 yr)
15
P/LP submissions
0%
P/LP missense
0.76
LOEUF
DN
Mechanism· predicted
Clinical Summary— C1QL3
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.52) — some intolerance to loss-of-function variants.
📋
ClinVar Variants
15 unique Pathogenic / Likely Pathogenic· 34 VUS of 58 total submissions
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.76LOEUF
pLI 0.516
Z-score 1.94
OE 0.16 (0.06–0.76)
Moderately constrained

Typical tolerance to LoF variation

Missense Constraint
2.12Z-score
OE missense 0.49 (0.40–0.60)
65 obs / 133.9 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.16 (0.06–0.76)
0≤0.351.4
Missense OE0.49 (0.40–0.60)
0≤0.61.4
Synonymous OE0.89
0≤1.21.6
LoF obs/exp: 1 / 6.2Missense obs/exp: 65 / 133.9Syn Z: 0.69
DN
0.6839th %ile
GOF
0.5268th %ile
LOF
0.50top 25%

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

58 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic15
VUS34
Likely Benign1
Benign3
15
Pathogenic
34
VUS
1
Likely Benign
3
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
15
0
15
Likely Pathogenic
0
0
0
0
0
VUS
0
28
6
0
34
Likely Benign
0
0
1
0
1
Benign
0
0
2
1
3
Total02824153

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

C1QL3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 4 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 2 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients