IQCJ

Summary

IQCJ (IQ motif containing J, HGNC:32406) is a protein-coding gene on chromosome 3q25.32, encoding IQ domain-containing protein J (Q1A5X6).

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 26 total
• MANE Select transcript: NM_001042706

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32406
Approved symbol	IQCJ
Name	IQ motif containing J
Location	3q25.32
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000214216
Ensembl biotype	protein_coding
OMIM	611622
Entrez	654502

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000397832, ENST00000451172, ENST00000481796, ENST00000482126

RefSeq mRNA: 3 — MANE Select: NM_001042706 NM_001042705, NM_001042706, NM_001197100

CCDS: CCDS46946, CCDS46947, CCDS56290

Canonical transcript exons

ENST00000397832 — 4 exons

Exon	Start	End
ENSE00001530409	159262548	159263747
ENSE00003549013	159252727	159252807
ENSE00003685529	159245843	159245907
ENSE00003909996	159069319	159069441

Expression profiles

Bgee: expression breadth broad, 46 present calls, max score 98.88.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3143 / max 57.4145, expressed in 90 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
39525	0.2283	81
39527	0.0807	44
39522	0.0053	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	98.88	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.24	gold quality
corpus callosum	UBERON:0002336	65.50	gold quality
pituitary gland	UBERON:0000007	48.50	gold quality
superior frontal gyrus	UBERON:0002661	48.44	gold quality
colonic epithelium	UBERON:0000397	46.66	gold quality
adenohypophysis	UBERON:0002196	45.28	gold quality
sural nerve	UBERON:0015488	43.04	gold quality
primary visual cortex	UBERON:0002436	42.99	silver quality
prefrontal cortex	UBERON:0000451	41.80	gold quality
skeletal muscle tissue	UBERON:0001134	41.50	silver quality
apex of heart	UBERON:0002098	41.26	silver quality
cortical plate	UBERON:0005343	41.20	gold quality
right testis	UBERON:0004534	40.59	gold quality
left testis	UBERON:0004533	40.50	gold quality
testis	UBERON:0000473	39.96	gold quality
frontal cortex	UBERON:0001870	39.34	gold quality
amygdala	UBERON:0001876	39.30	gold quality
temporal lobe	UBERON:0001871	39.18	gold quality
lower esophagus mucosa	UBERON:0035834	38.78	gold quality
Ammon’s horn	UBERON:0001954	38.44	gold quality
cerebral cortex	UBERON:0000956	37.94	gold quality
right atrium auricular region	UBERON:0006631	37.54	gold quality
Brodmann (1909) area 9	UBERON:0013540	37.25	gold quality
muscle tissue	UBERON:0002385	37.03	silver quality
brain	UBERON:0000955	36.96	gold quality
putamen	UBERON:0001874	36.65	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	36.32	silver quality
hindlimb stylopod muscle	UBERON:0004252	36.26	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.78

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• identification of SNPs within the IQCJ, NXPH1, PHF17 and MYB genes partly explaining the large interindividual variability observed in plasma triglyceride levels in response to an n-3 fatty acid supplementation (PMID:27160456)
• A genome-wide association study (GWAS) identified loci associated with the plasma triglyceride (TG) response to omega-3 fatty acid (FA) supplementation in IQCJ, NXPH1, PHF17 and MYB. (PMID:28134766)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Iqcj	ENSMUSG00000051777
rattus_norvegicus	Iqcj	ENSRNOG00000083869

Protein

Protein identifiers

IQ domain-containing protein J — Q1A5X6 (reviewed: Q1A5X6)

All UniProt accessions (2): A0AAQ5BIJ8, Q1A5X6

Isoforms (5)

UniProt ID	Names	Canonical?
Q1A5X6-1	IQCJ-1	yes
Q1A5X6-2	IQCJ-2
Q1A5X6-3	IQCJ-3
B3KU38-1	IQCJ-SCHIP1-1
B3KU38-2	IQCJ-SCHIP1-2

RefSeq proteins (3): NP_001036170, NP_001036171, NP_001184029 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029362	IQCJ-SCHIP1_N	Domain
IPR053113	IQ_domain_protein	Family

Pfam: PF15157

UniProt features (6 total): splice variant 2, chain 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q1A5X6-F1	49.01	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 25 (showing top): MIKKELSEN_MCV6_ICP_WITH_H3K27ME3, chr3q25, ZIM3_TARGET_GENES, MIR340_5P, MIR1297, MIR6833_3P, MIR26A_5P, MIR26B_5P, MIR4477A, MIR4465, MIR3714, MIR4768_5P, MIR6844, MIR218_5P, MIR7152_5P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

278 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IQCJ	F8WDG0	F8WDG0	932
IQCJ	NRGN	Q92686	750
IQCJ	GAP43	P17677	590
IQCJ	PRR23A	A6NEV1	584
IQCJ	NF2	P35240	563
IQCJ	POU2AF2	Q8IXP5	480
IQCJ	EXOC3L4	Q17RC7	467
IQCJ	HEATR5A	Q86XA9	462
IQCJ	CFAP263	Q9H0I3	434
IQCJ	CAPSL	Q8WWF8	430
IQCJ	TMEM39A	Q9NV64	419
IQCJ	NXPH1	P58417	414
IQCJ	NUDT12	Q9BQG2	398
IQCJ	MACIR	Q96GV9	398
IQCJ	YPEL5	P62699	370

IntAct

0 interactions, top by confidence:

BioGRID (2): IQCJ (Positive Genetic), IQCJ (Affinity Capture-MS)

ESM2 similar proteins: A2AGX3, A2T928, A2VDM8, A6NFK2, C4A0D9, D2CLZ9, D3ZHS6, E5DG73, E9Q6D6, F4JI46, P0CW19, P0CW20, P0DM64, P57769, Q071E0, Q1A5X6, Q2YDF2, Q4KLN5, Q52L14, Q5E9K2, Q5F3N6, Q5GH59, Q5RF96, Q5VT97, Q5VUJ9, Q66JB6, Q68EY3, Q6QB00, Q7TP98, Q80TL0, Q80ZW0, Q8C080, Q8NCT3, Q8WY54, Q92560, Q96ET8, Q96KN8, Q96MD7, Q96P26, Q99PU7

Diamond homologs: A0A088MLT8, A8DYY6, B3KU38, P0DPB3, P0DPB4, Q1A5X6, Q8BPW0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	26
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1722 predictions. Top by Δscore:

Variant	Effect	Δscore
3:159198928:G:A	acceptor_gain	1.0000
3:159245837:TCACA:T	acceptor_loss	1.0000
3:159245838:CACAG:C	acceptor_loss	1.0000
3:159245839:A:AG	acceptor_gain	1.0000
3:159245840:C:G	acceptor_gain	1.0000
3:159245840:CAG:C	acceptor_loss	1.0000
3:159245841:A:AG	acceptor_gain	1.0000
3:159245841:AGGA:A	acceptor_loss	1.0000
3:159245842:G:GA	acceptor_loss	1.0000
3:159245842:G:GG	acceptor_gain	1.0000
3:159245842:GGAA:G	acceptor_gain	1.0000
3:159245903:GAAAA:G	donor_gain	1.0000
3:159245904:AAAAG:A	donor_loss	1.0000
3:159245906:AAG:A	donor_loss	1.0000
3:159245907:AGTA:A	donor_loss	1.0000
3:159245908:G:GG	donor_gain	1.0000
3:159245908:GTAA:G	donor_loss	1.0000
3:159245909:T:A	donor_loss	1.0000
3:159245910:AA:A	donor_loss	1.0000
3:159252725:A:AG	acceptor_gain	1.0000
3:159252726:G:GG	acceptor_gain	1.0000
3:159262537:T:TA	acceptor_gain	1.0000
3:159262546:A:AG	acceptor_gain	1.0000
3:159262547:G:GG	acceptor_gain	1.0000
3:159262547:GC:G	acceptor_gain	1.0000
3:159262547:GCAT:G	acceptor_gain	1.0000
3:159069416:GTTCC:G	donor_gain	0.9900
3:159069437:GTCTG:G	donor_gain	0.9900
3:159198927:T:TA	acceptor_gain	0.9900
3:159242533:G:GT	donor_gain	0.9900

AlphaMissense

734 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:159262561:T:A	W57R	0.991
3:159262561:T:C	W57R	0.991
3:159262563:G:C	W57C	0.982
3:159262563:G:T	W57C	0.982
3:159262562:G:C	W57S	0.970
3:159262550:T:A	I53N	0.963
3:159262561:T:G	W57G	0.963
3:159262556:G:C	R55P	0.960
3:159262558:G:C	A56P	0.954
3:159262651:A:C	S87R	0.951
3:159262653:C:A	S87R	0.951
3:159262653:C:G	S87R	0.951
3:159262550:T:G	I53S	0.950
3:159262553:A:C	Q54P	0.949
3:159262550:T:C	I53T	0.941
3:159262565:G:C	R58P	0.935
3:159262639:A:C	S83R	0.913
3:159262641:C:A	S83R	0.913
3:159262641:C:G	S83R	0.913
3:159262562:G:T	W57L	0.912
3:159262675:A:C	S95R	0.879
3:159262677:C:A	S95R	0.879
3:159262677:C:G	S95R	0.879
3:159262554:G:C	Q54H	0.865
3:159262554:G:T	Q54H	0.865
3:159262603:A:C	S71R	0.833
3:159262605:C:A	S71R	0.833
3:159262605:C:G	S71R	0.833
3:159262574:T:C	L61P	0.830
3:159262570:T:G	Y60D	0.826

dbSNP variants (sampled 300 via entrez): RS1000006167 (3:159111352 C>G), RS1000006557 (3:159175792 T>C), RS1000007942 (3:159140493 T>C), RS1000022364 (3:159169319 T>C,G), RS1000032456 (3:159227379 T>C), RS1000033551 (3:159168634 A>T), RS1000059052 (3:159071106 A>G), RS1000065542 (3:159213177 A>G), RS1000079263 (3:159118637 C>A), RS1000091681 (3:159084712 A>G,T), RS1000110864 (3:159104423 C>T), RS1000116231 (3:159254718 C>G), RS1000133154 (3:159118422 A>G), RS1000149343 (3:159168924 C>T), RS1000152372 (3:159205640 C>T)

Disease associations

OMIM: gene MIM:611622 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST003264_181	Post bronchodilator FEV1/FVC ratio	3.000000e-06
GCST003264_919	Post bronchodilator FEV1/FVC ratio	1.000000e-06
GCST004721_15	Congenital heart disease (maternal effect)	3.000000e-06
GCST004721_16	Congenital heart disease (maternal effect)	7.000000e-06
GCST004723_13	Conotruncal heart defects (maternal effects)	8.000000e-06
GCST004723_19	Conotruncal heart defects (maternal effects)	3.000000e-06
GCST009310_33	Sensorimotor dexterity	9.000000e-07
GCST011823_2	Parkinson’s disease progression (cognitive)	3.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004713	FEV/FVC ratio
EFO:0008354	cognitive function measurement
EFO:0008336	disease progression measurement

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
Benzo(a)pyrene	affects methylation, increases methylation	2
benzo(e)pyrene	increases methylation	1
Methapyrilene	increases methylation	1

Clinical trials (associated diseases)

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