IQCF3

Summary

IQCF3 (IQ motif containing F3, HGNC:31816) is a protein-coding gene on chromosome 3p21.2, encoding IQ domain-containing protein F3 (P0C7M6).

Predicted to enable calmodulin binding activity.

Source: NCBI Gene 401067 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 28 total
• MANE Select transcript: NM_001393887

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31816
Approved symbol	IQCF3
Name	IQ motif containing F3
Location	3p21.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000229972
Ensembl biotype	protein_coding
Entrez	401067

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 4 protein_coding, 2 protein_coding_CDS_not_defined, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000437810, ENST00000440739, ENST00000444293, ENST00000446775, ENST00000462079, ENST00000465028, ENST00000472485, ENST00000474242, ENST00000660642

RefSeq mRNA: 3 — MANE Select: NM_001393887 NM_001085479, NM_001207023, NM_001393887

CCDS: CCDS46837

Canonical transcript exons

ENST00000440739 — 3 exons

Exon	Start	End
ENSE00001855227	51830403	51830856
ENSE00003831508	51829665	51829712
ENSE00003934679	51829426	51829493

Expression profiles

Bgee: expression breadth broad, 81 present calls, max score 96.19.

Top tissues by expression

110 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	96.19	gold quality
right testis	UBERON:0004534	96.06	gold quality
testis	UBERON:0000473	95.64	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.48	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	75.60	gold quality
superior frontal gyrus	UBERON:0002661	58.25	gold quality
Brodmann (1909) area 9	UBERON:0013540	49.04	gold quality
prefrontal cortex	UBERON:0000451	48.25	gold quality
frontal cortex	UBERON:0001870	48.25	gold quality
primary visual cortex	UBERON:0002436	47.02	gold quality
right frontal lobe	UBERON:0002810	46.81	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	46.19	gold quality
lower esophagus mucosa	UBERON:0035834	44.87	silver quality
metanephros cortex	UBERON:0010533	44.06	gold quality
cerebral cortex	UBERON:0000956	43.84	gold quality
fundus of stomach	UBERON:0001160	43.48	gold quality
colonic epithelium	UBERON:0000397	42.67	gold quality
granulocyte	CL:0000094	42.66	silver quality
ventricular zone	UBERON:0003053	42.08	gold quality
cortical plate	UBERON:0005343	39.91	gold quality
anterior cingulate cortex	UBERON:0009835	39.70	gold quality
right coronary artery	UBERON:0001625	39.36	silver quality
sural nerve	UBERON:0015488	38.56	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	36.96	gold quality
body of stomach	UBERON:0001161	36.67	gold quality
bone marrow	UBERON:0002371	36.42	silver quality
vermiform appendix	UBERON:0001154	36.29	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
stomach	UBERON:0000945	35.73	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.33

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Functional Annotations of Single-Nucleotide Polymorphism (SNP)-Based and Gene-Based Genome-Wide Association Studies Show Genes Affecting Keratitis Susceptibility. (PMID:32450567)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Iqcf3	ENSMUSG00001074846

Paralogs (4): IQCF1 (ENSG00000173389), IQCF2 (ENSG00000184345), IQCF5 (ENSG00000214681), IQCF6 (ENSG00000214686)

Protein

Protein identifiers

IQ domain-containing protein F3 — P0C7M6 (reviewed: P0C7M6)

All UniProt accessions (3): A0A590UJG8, F2Z334, P0C7M6

RefSeq proteins (3): NP_001078948, NP_001193952, NP_001380816* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000048	IQ_motif_EF-hand-BS	Binding_site
IPR039887	IQCF	Family

Pfam: PF00612

UniProt features (2 total): chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0C7M6-F1	84.59	0.68

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 12 (showing top): chr3p21, GSE11057_NAIVE_VS_CENT_MEMORY_CD4_TCELL_UP, POU2AF1_TARGET_GENES, DESCARTES_FETAL_CEREBRUM_EXCITATORY_NEURONS, BPTF_TARGET_GENES, GSE2706_UNSTIM_VS_2H_LPS_DC_UP, GSE6259_FLT3L_INDUCED_33D1_POS_DC_VS_CD8_TCELL_DN, GSE37301_HEMATOPOIETIC_STEM_CELL_VS_LYMPHOID_PRIMED_MPP_DN, GSE38697_LIGHT_ZONE_VS_DARK_ZONE_BCELL_DN, GOMF_CALMODULIN_BINDING, GSE41867_DAY15_EFFECTOR_VS_DAY30_MEMORY_CD8_TCELL_LCMV_ARMSTRONG_DN, GSE46606_DAY1_VS_DAY3_CD40L_IL2_IL5_STIMULATED_BCELL_DN

GO Biological Process (0):

GO Molecular Function (2): calmodulin binding (GO:0005516), protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein binding	1
binding	1

Protein interactions and networks

STRING

192 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IQCF3	C16orf90	A8MZG2	480
IQCF3	WFDC11	Q8NEX6	479
IQCF3	SPANXN5	Q5MJ07	446
IQCF3	PRAMEF12	O95522	431
IQCF3	TEX29	Q8N6K0	419
IQCF3	RGPD4	Q7Z3J3	413
IQCF3	DEFB112	Q30KQ8	402
IQCF3	LELP1	Q5T871	393
IQCF3	RAD51AP2	Q09MP3	377
IQCF3	PIERCE1	Q5BN46	376
IQCF3	TMED6	Q8WW62	370
IQCF3	CCDC112	Q8NEF3	370
IQCF3	DPH7	Q9BTV6	366
IQCF3	NEMP1	O14524	366
IQCF3	STARD6	P59095	352

IntAct

4 interactions, top by confidence:

A	B	Type	Score
IQCF3	UBQLN2	psi-mi:“MI:0915”(physical association)	0.560
IQCF3	UBQLN2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (2): NDFIP1 (Affinity Capture-MS), IQCF3 (Two-hybrid)

ESM2 similar proteins: A1IGU3, A1IGU4, A1IGU5, A5D8V7, A5PK16, A6QP29, A7E3N7, A8K8P3, A9CB34, B0KWR6, B5DFA1, D3ZI76, G3HQ82, O73770, P0C7M6, P41002, Q14129, Q14DK4, Q15051, Q3SYS7, Q3UK37, Q3UZY0, Q5SNV9, Q5SXM2, Q60953, Q60I26, Q60I27, Q69ZT1, Q6NUI2, Q8BP00, Q8BP86, Q8C1F5, Q8C2K1, Q8CJ00, Q8IV45, Q8NCU4, Q8NE28, Q8NEE8, Q8TE82, Q95KD7

Diamond homologs: A8MTL0, A8MYZ5, P0C7M6, Q2M2U5, Q32KU4, Q3SYS7, Q6AXX0, Q8IXL9, Q8N6M8, Q9D498, Q9D9K8, Q9DAL7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

28 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	21
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

748 predictions. Top by Δscore:

Variant	Effect	Δscore
3:51828288:G:GG	donor_gain	0.9800
3:51828571:TTTGC:T	donor_gain	0.9800
3:51829273:GAGA:G	acceptor_gain	0.9800
3:51828287:A:AG	donor_gain	0.9700
3:51828575:C:T	donor_gain	0.9600
3:51829489:GCTGT:G	donor_gain	0.9600
3:51829492:GT:G	donor_gain	0.9600
3:51829483:G:GG	donor_gain	0.9300
3:51829494:G:GG	donor_gain	0.9300
3:51828284:T:G	donor_gain	0.9200
3:51829482:A:AG	donor_gain	0.9200
3:51829444:G:GT	donor_gain	0.9000
3:51829662:CAGAA:C	acceptor_gain	0.9000
3:51829663:AGAAA:A	acceptor_gain	0.9000
3:51829664:GAAAG:G	acceptor_gain	0.9000
3:51828570:GTTT:G	donor_gain	0.8900
3:51828578:G:GG	donor_gain	0.8900
3:51829273:GA:G	acceptor_gain	0.8900
3:51828577:A:AG	donor_gain	0.8800
3:51828143:T:TA	acceptor_gain	0.8600
3:51829272:A:AG	acceptor_gain	0.8600
3:51829273:G:GG	acceptor_gain	0.8600
3:51829480:G:T	donor_gain	0.8600
3:51828263:A:T	donor_gain	0.8500
3:51828489:T:G	acceptor_gain	0.8500
3:51828226:G:GT	donor_gain	0.8300
3:51829487:A:G	donor_gain	0.8300
3:51830401:A:AG	acceptor_gain	0.8300
3:51830402:G:GG	acceptor_gain	0.8300
3:51828586:T:G	donor_gain	0.8100

AlphaMissense

1001 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:51830775:T:C	F147L	0.951
3:51830777:C:A	F147L	0.951
3:51830777:C:G	F147L	0.951
3:51830455:T:C	I40T	0.923
3:51830524:T:C	I63T	0.907
3:51830535:T:A	W67R	0.900
3:51830535:T:C	W67R	0.900
3:51830788:T:C	I151T	0.891
3:51830469:C:A	R45S	0.887
3:51830466:T:A	W44R	0.882
3:51830466:T:C	W44R	0.882
3:51830459:G:C	Q41H	0.874
3:51830459:G:T	Q41H	0.874
3:51830455:T:G	I40S	0.870
3:51830642:G:A	M102I	0.865
3:51830642:G:C	M102I	0.865
3:51830642:G:T	M102I	0.865
3:51830470:G:C	R45P	0.862
3:51830537:G:C	W67C	0.861
3:51830537:G:T	W67C	0.861
3:51830468:G:C	W44C	0.852
3:51830468:G:T	W44C	0.852
3:51830638:G:C	R101P	0.852
3:51830776:T:C	F147S	0.834
3:51830528:G:C	Q64H	0.832
3:51830528:G:T	Q64H	0.832
3:51830524:T:G	I63S	0.831
3:51830484:C:A	R50S	0.828
3:51830472:G:A	G46R	0.827
3:51830472:G:C	G46R	0.827

dbSNP variants (sampled 300 via entrez): RS1000359119 (3:51830773 A>G), RS1001246076 (3:51825201 A>G), RS1001535865 (3:51831134 G>A,T), RS1001867406 (3:51825393 C>T), RS1002251998 (3:51830442 G>A,C), RS1002641801 (3:51825807 A>G), RS1003102598 (3:51825997 A>G), RS1003324685 (3:51826846 T>C), RS1003701150 (3:51827579 T>C), RS1003920427 (3:51826729 C>G,T), RS1004049005 (3:51827312 C>T), RS1004272559 (3:51826312 C>G,T), RS1005599070 (3:51825150 C>T), RS1005925442 (3:51830173 T>C), RS1006487830 (3:51830341 A>G,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST010988_143	Adult body size	1.000000e-09

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
2-palmitoylglycerol	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.