IQCH

Summary

IQCH (IQ motif containing H, HGNC:25721) is a protein-coding gene on chromosome 15q23, encoding IQ domain-containing protein H (Q86VS3). May play a regulatory role in spermatogenesis.

Predicted to act upstream of or within lncRNA transcription and single fertilization. Predicted to be active in nuclear speck.

Source: NCBI Gene 64799 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 157 total
• MANE Select transcript: NM_001031715

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25721
Approved symbol	IQCH
Name	IQ motif containing H
Location	15q23
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12476
Ensembl gene	ENSG00000103599
Ensembl biotype	protein_coding
OMIM	612523
Entrez	64799

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 5 protein_coding, 4 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000335894, ENST00000512104, ENST00000514049, ENST00000535744, ENST00000558759, ENST00000559172, ENST00000559568, ENST00000560497, ENST00000560790, ENST00000561339, ENST00000561357, ENST00000629425

RefSeq mRNA: 11 — MANE Select: NM_001031715 NM_001031715, NM_001284347, NM_001284348, NM_001284349, NM_001322470, NM_001322471, NM_001322472, NM_001322473, NM_001322474, NM_001322475, NM_022784

CCDS: CCDS10223, CCDS32273, CCDS76772

Canonical transcript exons

ENST00000335894 — 21 exons

Exon	Start	End
ENSE00000942631	67395291	67395563
ENSE00001108116	67490003	67490064
ENSE00001198458	67254786	67254947
ENSE00003491688	67416931	67417051
ENSE00003514299	67465127	67465297
ENSE00003519660	67400114	67400305
ENSE00003532292	67359847	67359885
ENSE00003535229	67373367	67373433
ENSE00003536141	67261272	67261394
ENSE00003542724	67475696	67475818
ENSE00003549550	67494258	67494366
ENSE00003556075	67357345	67357421
ENSE00003582956	67500633	67501804
ENSE00003583398	67384936	67385019
ENSE00003591767	67372111	67372662
ENSE00003593744	67344063	67344191
ENSE00003597363	67263122	67263216
ENSE00003640209	67336975	67337095
ENSE00003640377	67279395	67279512
ENSE00003665413	67388831	67389006
ENSE00003681611	67421291	67421577

Expression profiles

Bgee: expression breadth ubiquitous, 181 present calls, max score 90.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 1.9204 / max 80.0551, expressed in 955 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
147343	1.0011	547
147342	0.8387	546
147346	0.0519	11
147344	0.0176	2
147345	0.0111	3

Top tissues by expression

284 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	90.93	gold quality
buccal mucosa cell	CL:0002336	86.01	gold quality
bronchial epithelial cell	CL:0002328	84.80	gold quality
right uterine tube	UBERON:0001302	81.53	gold quality
sperm	CL:0000019	80.38	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.42	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	79.17	gold quality
epithelium of bronchus	UBERON:0002031	79.01	gold quality
male germ cell	CL:0000015	77.85	silver quality
bronchus	UBERON:0002185	77.65	gold quality
left testis	UBERON:0004533	77.63	gold quality
testis	UBERON:0000473	77.39	gold quality
right testis	UBERON:0004534	77.28	gold quality
islet of Langerhans	UBERON:0000006	70.64	gold quality
adenohypophysis	UBERON:0002196	69.43	gold quality
left lobe of thyroid gland	UBERON:0001120	68.64	gold quality
thyroid gland	UBERON:0002046	68.64	gold quality
pituitary gland	UBERON:0000007	68.40	gold quality
mucosa of paranasal sinus	UBERON:0005030	68.26	silver quality
calcaneal tendon	UBERON:0003701	68.00	gold quality
adrenal tissue	UBERON:0018303	67.53	gold quality
right lobe of thyroid gland	UBERON:0001119	67.42	gold quality
secondary oocyte	CL:0000655	66.98	gold quality
stromal cell of endometrium	CL:0002255	66.95	gold quality
oocyte	CL:0000023	66.47	gold quality
metanephros cortex	UBERON:0010533	66.16	gold quality
sural nerve	UBERON:0015488	66.01	gold quality
fallopian tube	UBERON:0003889	65.63	gold quality
tendon	UBERON:0000043	64.92	gold quality
epithelium of nasopharynx	UBERON:0001951	64.44	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting IQCH, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-498-5P	99.76	69.64	1807
HSA-MIR-4677-5P	99.70	70.09	1940
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-586	99.65	70.40	2051
HSA-MIR-330-3P	99.41	69.95	2521
HSA-MIR-3978	99.24	68.39	2201
HSA-MIR-6739-3P	99.22	68.84	1843
HSA-MIR-3908	98.75	67.31	1160
HSA-MIR-3944-5P	98.50	67.55	997
HSA-MIR-1243	97.07	65.44	719
HSA-MIR-582-3P	96.69	67.38	1019
HSA-MIR-376A-2-5P	96.43	68.06	715
HSA-MIR-217-3P	95.67	68.42	1000
HSA-MIR-6753-5P	94.70	64.08	470

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	iqch	ENSDARG00000015476
mus_musculus	Iqch	ENSMUSG00000037801
rattus_norvegicus	Iqch	ENSRNOG00000008353

Protein

Protein identifiers

IQ domain-containing protein H — Q86VS3 (reviewed: Q86VS3)

Alternative names: Testis development protein NYD-SP5

All UniProt accessions (7): Q86VS3, B4E2J4, D6RGG0, H0YMU5, H3BMH8, H3BRL4, H3BU17

UniProt curated annotations — full annotation on UniProt →

Function. May play a regulatory role in spermatogenesis.

Tissue specificity. Expressed in fetal and adult testis, in germ cells but not somatic cells.

Isoforms (5)

UniProt ID	Names	Canonical?
Q86VS3-1	1	yes
Q86VS3-2	2
Q86VS3-3	3
Q86VS3-4	4
Q86VS3-5	5

RefSeq proteins (11): NP_001026885, NP_001271276, NP_001271277, NP_001271278, NP_001309399, NP_001309400, NP_001309401, NP_001309402, NP_001309403, NP_001309404, NP_073621 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038752	IQCH	Family
IPR056855	ATP-grasp_IQCH	Domain

Pfam: PF24923

UniProt features (18 total): splice variant 11, region of interest 2, chain 1, domain 1, sequence variant 1, sequence conflict 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86VS3-F1	78.09	0.48

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 118 (showing top): GOBP_SINGLE_FERTILIZATION, TANAKA_METHYLATED_IN_ESOPHAGEAL_CARCINOMA, GOBP_FERTILIZATION, chr15q23, GOCC_NUCLEAR_SPECK, GOCC_NUCLEAR_BODY, GOCC_RIBONUCLEOPROTEIN_GRANULE, SCGGAAGY_ELK1_02, ZHOU_INFLAMMATORY_RESPONSE_LIVE_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN, BRUINS_UVC_RESPONSE_LATE, GOCC_SUPRAMOLECULAR_COMPLEX, ASH1L_TARGET_GENES, CIITA_TARGET_GENES

GO Biological Process (4): single fertilization (GO:0007338), lncRNA transcription (GO:0140742), biological_process (GO:0008150), gene expression (GO:0010467)

GO Molecular Function (1): molecular_function (GO:0003674)

GO Cellular Component (2): nuclear speck (GO:0016607), cellular_component (GO:0005575)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
fertilization	1
DNA-templated transcription	1
macromolecule biosynthetic process	1
nuclear ribonucleoprotein granule	1

Protein interactions and networks

STRING

416 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IQCH	LDHA	P00338	769
IQCH	TESMIN	Q9Y4I5	447
IQCH	SPATA16	Q9BXB7	400
IQCH	CATSPER1	Q8NEC5	366
IQCH	FEM1B	Q9UK73	351
IQCH	TMTC1	Q8IUR5	321
IQCH	FER1L5	A0AVI2	257
IQCH	SLC25A31	Q9H0C2	252
IQCH	CATSPERD	Q86XM0	251
IQCH	DMRT1	Q9Y5R6	248
IQCH	PKDREJ	Q9NTG1	247
IQCH	SLC25A26	Q70HW3	242
IQCH	AASDH	Q4L235	240
IQCH	PEG3	P78418	228
IQCH	CATSPERB	Q9H7T0	227

IntAct

5 interactions, top by confidence:

A	B	Type	Score
IQCH	COL6A2	psi-mi:“MI:0915”(physical association)	0.400
IQCH	MTHFD1	psi-mi:“MI:0915”(physical association)	0.400
NEK4	E2F8	psi-mi:“MI:0914”(association)	0.350
	DDX3Y	psi-mi:“MI:0914”(association)	0.350

BioGRID (8): CBX6 (Affinity Capture-MS), IQCH (Reconstituted Complex), IQCH (Synthetic Lethality), IQCH (Proximity Label-MS), IQCH (Proximity Label-MS), IQCH (Affinity Capture-MS), IQCH (Affinity Capture-RNA), APP (Reconstituted Complex)

ESM2 similar proteins: A0A1S4D1D3, A0A1W2PR95, A0A8I6ASZ5, A8WE67, D2K8N5, D3Z8X7, D3ZND0, E1C760, E7EXT2, F6Y9J3, F7AEX0, O08836, O60308, P27641, P54729, P78318, Q0P4W3, Q14CX7, Q15021, Q2QY04, Q2YD98, Q3ZC62, Q4V8E4, Q5EAU9, Q61249, Q68FJ0, Q6NY52, Q6PBQ2, Q6PGY6, Q6QI44, Q7ZXA8, Q80V31, Q86VS3, Q8BWZ3, Q8C6E0, Q8C9J3, Q8IYW2, Q8K2Z4, Q8LDQ4, Q8LNU5

Diamond homologs: Q1LXZ7, Q86VS3, Q9D2K4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	120
Likely benign	20
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

6786 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:67395319:T:C	L554P	0.995
15:67395327:A:C	S557R	0.995
15:67395329:T:A	S557R	0.995
15:67395329:T:G	S557R	0.995
15:67395420:G:C	A588P	0.995
15:67400165:T:A	W653R	0.994
15:67400165:T:C	W653R	0.994
15:67372489:G:C	A378P	0.993
15:67395421:C:A	A588D	0.992
15:67373382:T:A	W441R	0.991
15:67373382:T:C	W441R	0.991
15:67373416:T:A	I452N	0.991
15:67417018:T:A	W729R	0.991
15:67417018:T:C	W729R	0.991
15:67372655:G:C	R433P	0.990
15:67385002:G:C	R480T	0.990
15:67385003:G:C	R480S	0.990
15:67385003:G:T	R480S	0.990
15:67373408:G:C	R449S	0.988
15:67373408:G:T	R449S	0.988
15:67494308:T:C	L971P	0.987
15:67372495:T:A	W380R	0.986
15:67372495:T:C	W380R	0.986
15:67372240:T:A	W295R	0.985
15:67372240:T:C	W295R	0.985
15:67372283:T:C	L309P	0.985
15:67400207:G:C	A667P	0.985
15:67421548:T:C	F826L	0.985
15:67421550:T:A	F826L	0.985
15:67421550:T:G	F826L	0.985

dbSNP variants (sampled 300 via entrez): RS1000004452 (15:67342026 C>T), RS1000031142 (15:67436569 C>G,T), RS1000049406 (15:67291667 T>C), RS1000055887 (15:67485419 A>G), RS1000067544 (15:67337409 C>A), RS1000073173 (15:67264848 C>G), RS1000077292 (15:67388682 T>C), RS1000097606 (15:67382860 A>G), RS1000102937 (15:67500119 T>C), RS1000107719 (15:67446795 A>T), RS1000115106 (15:67482779 C>T), RS1000139503 (15:67432769 C>T), RS1000143118 (15:67289013 C>T), RS1000149785 (15:67343602 T>G), RS1000155936 (15:67298404 A>G)

Disease associations

OMIM: gene MIM:612523 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression	2
methylmercuric chloride	decreases expression	1
propionaldehyde	increases expression	1
bisphenol A	affects expression	1
sodium arsenite	increases abundance, affects cotreatment, decreases expression	1
butyraldehyde	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
pentanal	decreases expression	1
CGP 52608	increases reaction, affects binding	1
entinostat	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	decreases methylation	1
Arsenic Trioxide	increases expression	1
Leflunomide	increases expression	1
Arsenic	decreases expression, increases abundance, affects cotreatment	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
N-Nitrosopyrrolidine	decreases expression	1
Phenylmercuric Acetate	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Valproic Acid	increases expression	1
Cyclosporine	increases expression	1

Clinical trials (associated diseases)

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