C1QTNF9

Chr 13

C1q and TNF related 9

Also known as: AQL1, C1QTNF9A, CTRP9

NCBI Gene: 338872 ENSG00000240654 UniProt: P0C862

The protein is a probable adipokine that activates AMPK, AKT, and p44/42 MAPK signaling pathways and enables identical protein binding activity. Mutations cause autosomal recessive intellectual disability with macrocephaly, seizures, and speech delay. The gene is not highly constrained against loss-of-function variants.

ResearchSummary from RefSeq, UniProt

Enables identical protein binding activity. Predicted to be involved in signal transduction. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Jun 2026]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.29

LOEUF

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.29LOEUF

pLI 0.000

Z-score 0.84

OE 0.74 (0.45–1.29)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.57Z-score

OE missense 0.88 (0.77–1.00)

156 obs / 177.3 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.74 (0.45–1.29)

0≤0.351.4

Missense OE?0.88 (0.77–1.00)

0≤0.61.4

Synonymous OE?0.93

0≤1.21.6

LoF obs/exp: 9 / 12.1Missense obs/exp: 156 / 177.3Syn Z: 0.45

Background carrier burden — how many people carry a rare variant somewhere in C1QTNF9?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 160

252 rare PASS variants

Rare truncating (LoF)

1 in 1,000

28 rare PASS variants

Rare synonymous (reference)

1 in 110

113 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for C1QTNF9. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 220	1 in 2,300
South Asian	~43k	1 in 76	1 in 1,100
Remaining (unassigned)	~30k	1 in 120	1 in 1,700
European (Finnish)	~27k	1 in 330	none seen
Admixed American	~22k	1 in 140	1 in 1,300
African / African American	~21k	1 in 74	1 in 390
East Asian	~20k	1 in 120	none seen
Ashkenazi Jewish	~13k	1 in 630	none seen
Middle Eastern	~2,884	1 in 130	≈ 1 in 720

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 2 of 3 coding exons well covered in gnomAD exomes; exon 4 marginal. Genomes: 1 of 3 (exons 2, 4 below).? see exons ↓