LRRIQ4

Summary

LRRIQ4 (leucine rich repeats and IQ motif containing 4, HGNC:34298) is a protein-coding gene on chromosome 3q26.2, encoding Leucine-rich repeat and IQ domain-containing protein 4 (A6NIV6).

Predicted to be active in cytoplasm.

Source: NCBI Gene 344657 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 101 total
• MANE Select transcript: NM_001080460

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34298
Approved symbol	LRRIQ4
Name	leucine rich repeats and IQ motif containing 4
Location	3q26.2
Locus type	gene with protein product
Status	Approved
Aliases	LRRC64
Ensembl gene	ENSG00000188306
Ensembl biotype	protein_coding
Entrez	344657

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000340806, ENST00000691416

RefSeq mRNA: 1 — MANE Select: NM_001080460 NM_001080460

CCDS: CCDS46951

Canonical transcript exons

ENST00000340806 — 6 exons

Exon	Start	End
ENSE00001365278	169821891	169822941
ENSE00001369076	169832987	169833183
ENSE00001370722	169837479	169837773
ENSE00001380992	169830492	169830630
ENSE00001382770	169828759	169828932
ENSE00003927530	169812870	169813046

Expression profiles

Bgee: expression breadth broad, 39 present calls, max score 78.22.

Top tissues by expression

108 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	78.22	silver quality
rectum	UBERON:0001052	62.36	gold quality
left testis	UBERON:0004533	57.41	gold quality
testis	UBERON:0000473	57.38	gold quality
right testis	UBERON:0004534	56.89	gold quality
mucosa of transverse colon	UBERON:0004991	56.69	gold quality
transverse colon	UBERON:0001157	49.15	gold quality
duodenum	UBERON:0002114	48.90	gold quality
endometrium	UBERON:0001295	48.43	silver quality
colonic epithelium	UBERON:0000397	45.20	gold quality
vermiform appendix	UBERON:0001154	44.85	gold quality
hindlimb stylopod muscle	UBERON:0004252	42.47	gold quality
intestine	UBERON:0000160	42.19	gold quality
small intestine	UBERON:0002108	42.13	gold quality
colon	UBERON:0001155	41.99	gold quality
right uterine tube	UBERON:0001302	41.62	silver quality
body of stomach	UBERON:0001161	41.38	gold quality
stomach	UBERON:0000945	41.28	gold quality
small intestine Peyer’s patch	UBERON:0003454	41.16	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	40.80	silver quality
bone marrow cell	CL:0002092	40.40	gold quality
fallopian tube	UBERON:0003889	39.43	gold quality
lower esophagus mucosa	UBERON:0035834	39.12	gold quality
prefrontal cortex	UBERON:0000451	39.08	silver quality
fundus of stomach	UBERON:0001160	39.06	gold quality
ganglionic eminence	UBERON:0004023	39.05	gold quality
saliva-secreting gland	UBERON:0001044	38.62	gold quality
lymph node	UBERON:0000029	38.54	silver quality
minor salivary gland	UBERON:0001830	38.43	gold quality
right lung	UBERON:0002167	38.22	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.95

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting LRRIQ4, 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-4789-3P	99.99	70.75	2484
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-2681-5P	99.75	67.64	1655
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-545-5P	99.66	70.18	2308
HSA-MIR-4672	99.50	71.58	2893
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-4735-5P	99.43	68.49	1780
HSA-MIR-222-5P	98.75	69.17	1242
HSA-MIR-384	98.71	67.34	1229
HSA-MIR-15B-3P	97.85	66.68	974
HSA-MIR-6798-3P	94.55	68.78	325

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lrriq4	ENSMUSG00000027703
rattus_norvegicus	Lrriq4	ENSRNOG00000009004

Paralogs (31): LRRC7 (ENSG00000033122), PHLPP2 (ENSG00000040199), LRRC40 (ENSG00000066557), LRCH4 (ENSG00000077454), PHLPP1 (ENSG00000081913), SHOC2 (ENSG00000108061), ERBIN (ENSG00000112851), LRRC39 (ENSG00000122477), LRCH2 (ENSG00000130224), LRCH1 (ENSG00000136141), LRRC8A (ENSG00000136802), LRRC1 (ENSG00000137269), MFHAS1 (ENSG00000147324), LRRC27 (ENSG00000148814), LRRK1 (ENSG00000154237), LRRC58 (ENSG00000163428), LRRC2 (ENSG00000163827), LRRC18 (ENSG00000165383), LRRC28 (ENSG00000168904), LRRC8E (ENSG00000171017), LRRC8C (ENSG00000171488), LRRC8D (ENSG00000171492), PIDD1 (ENSG00000177595), SCRIB (ENSG00000180900), LRCH3 (ENSG00000186001), LRRC8B (ENSG00000197147), LRRC10 (ENSG00000198812), LRRC10B (ENSG00000204950), LRRC30 (ENSG00000206422), LRRC69 (ENSG00000214954), LRRD1 (ENSG00000240720)

Protein

Protein identifiers

Leucine-rich repeat and IQ domain-containing protein 4 — A6NIV6 (reviewed: A6NIV6)

Alternative names: Leucine-rich repeat-containing protein 64

All UniProt accessions (2): A6NIV6, A0A8I5KNZ9

RefSeq proteins (1): NP_001073929* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001611	Leu-rich_rpt	Repeat
IPR003591	Leu-rich_rpt_typical-subtyp	Repeat
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR050216	LRR_domain-containing	Family
IPR055414	LRR_R13L4/SHOC2-like	Domain

Pfam: PF13855, PF23598

UniProt features (26 total): repeat 20, region of interest 2, chain 1, domain 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NIV6-F1	90.00	0.84

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 30 (showing top): chr3q26, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B, MIR4729, MIR466, MIR4789_3P, MIR545_5P, GSE15733_BM_VS_SPLEEN_MEMORY_CD4_TCELL_UP, GSE15750_WT_VS_TRAF6KO_DAY6_EFF_CD8_TCELL_DN, GSE17721_CTRL_VS_LPS_12H_BMDC_UP, GSE17721_PAM3CSK4_VS_CPG_1H_BMDC_UP, DESCARTES_MAIN_FETAL_SATB2_LRRC7_POSITIVE_CELLS, DESCARTES_FETAL_LIVER_VASCULAR_ENDOTHELIAL_CELLS, GSE17721_LPS_VS_GARDIQUIMOD_4H_BMDC_DN, GSE20366_EX_VIVO_VS_DEC205_CONVERSION_NAIVE_CD4_TCELL_DN, GSE32423_CTRL_VS_IL4_MEMORY_CD8_TCELL_DN

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

552 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRIQ4	LRRC34	Q8IZ02	731
LRRIQ4	ACTRT3	Q9BYD9	730
LRRIQ4	MYNN	Q9NPC7	721
LRRIQ4	LRRC31	Q6UY01	695
LRRIQ4	DCAF4	Q8WV16	464
LRRIQ4	INSYN2B	A6NMK8	447
LRRIQ4	CFAP119	A1A4V9	445
LRRIQ4	TMEM174	Q8WUU8	435
LRRIQ4	ETV3L	Q6ZN32	418
LRRIQ4	KIAA1671	Q9BY89	392
LRRIQ4	CREG2	Q8IUH2	391
LRRIQ4	PRR14	Q9BWN1	366
LRRIQ4	RBMXL3	Q8N7X1	362
LRRIQ4	PRSS53	Q2L4Q9	355
LRRIQ4	PHTF2	Q8N3S3	355

IntAct

4 interactions, top by confidence:

A	B	Type	Score
LRRIQ4	HMGN2	psi-mi:“MI:0915”(physical association)	0.400
NFKB1	NFKB1	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350

BioGRID (3): LRRIQ4 (Affinity Capture-MS), HMGN2 (Proximity Label-MS), LRRIQ4 (Affinity Capture-MS)

ESM2 similar proteins: A4D1F6, A4IIK1, A6H6A4, A6NIV6, A6NM36, C0STK7, D3ZXS4, F1R6I3, F6R2G2, P14605, Q09562, Q32KX5, Q38SD2, Q3TX51, Q3UHC2, Q3UV48, Q3ZC49, Q4R6F0, Q54AX5, Q58A48, Q5G5E0, Q62192, Q65YW8, Q65Z91, Q66HD6, Q6AXL3, Q6GLE8, Q6GM71, Q6R5N8, Q6ZNQ3, Q7Z2Q7, Q86X40, Q8BGI7, Q8C0R9, Q8N456, Q8VDB8, Q96DD0, Q99467, Q99MB1, Q9BYS8

Diamond homologs: A6H6A4, A6NIV6, Q4V8I7, Q80WG5, Q8IWT6, A5PK13, Q3KRC6, Q498T9, Q5DU41, Q5U308, Q66JT1, Q68F79, Q6NSJ5, Q6NU09, Q6P9F7, Q7L1W4, Q8BGR2, Q8R502, Q8TDW0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	95
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

704 predictions. Top by Δscore:

Variant	Effect	Δscore
3:169822940:AGGT:A	donor_loss	1.0000
3:169822941:GGTA:G	donor_loss	1.0000
3:169822942:G:GC	donor_loss	1.0000
3:169822943:T:A	donor_loss	1.0000
3:169822937:GACAG:G	donor_gain	0.9900
3:169830491:GA:G	acceptor_gain	0.9900
3:169832953:A:G	acceptor_gain	0.9900
3:169832985:A:AG	acceptor_gain	0.9900
3:169832986:G:GG	acceptor_gain	0.9900
3:169832986:GCTTT:G	acceptor_gain	0.9900
3:169833165:GAATA:G	donor_gain	0.9900
3:169833179:CAAAG:C	donor_loss	0.9900
3:169833180:AAAG:A	donor_loss	0.9900
3:169833181:AAG:A	donor_loss	0.9900
3:169833182:AGG:A	donor_loss	0.9900
3:169833183:GG:G	donor_loss	0.9900
3:169833184:GTAAA:G	donor_loss	0.9900
3:169833185:T:A	donor_loss	0.9900
3:169822942:G:GG	donor_gain	0.9800
3:169830490:A:AG	acceptor_gain	0.9800
3:169830491:G:GG	acceptor_gain	0.9800
3:169832982:TTCA:T	acceptor_loss	0.9800
3:169832983:TCA:T	acceptor_loss	0.9800
3:169833151:G:GT	donor_gain	0.9800
3:169833165:G:GT	donor_loss	0.9800
3:169833166:A:T	donor_gain	0.9800
3:169830486:T:G	acceptor_loss	0.9700
3:169830487:TTCA:T	acceptor_loss	0.9700
3:169830488:TCA:T	acceptor_loss	0.9700
3:169830490:AGAG:A	acceptor_loss	0.9700

AlphaMissense

3666 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:169822292:G:C	R124P	0.982
3:169822289:T:C	L123P	0.974
3:169822358:T:C	L146P	0.972
3:169822148:T:C	L76P	0.966
3:169828868:T:C	L377S	0.965
3:169830579:T:C	C428R	0.963
3:169822217:T:C	L99P	0.962
3:169822223:T:C	L101P	0.962
3:169822515:C:A	N198K	0.961
3:169822515:C:G	N198K	0.961
3:169822421:T:C	L167P	0.959
3:169822289:T:A	L123H	0.957
3:169832999:T:C	L449S	0.957
3:169822505:T:C	L195P	0.956
3:169822367:T:C	L149P	0.955
3:169822148:T:A	L76H	0.954
3:169822006:T:C	F29L	0.952
3:169822008:C:A	F29L	0.952
3:169822008:C:G	F29L	0.952
3:169822436:T:C	L172P	0.951
3:169822164:C:A	N81K	0.950
3:169822164:C:G	N81K	0.950
3:169822154:T:C	L78P	0.949
3:169822226:G:T	S102I	0.948
3:169822514:A:T	N198I	0.946
3:169822283:G:C	R121P	0.944
3:169822289:T:G	L123R	0.944
3:169822225:A:C	S102R	0.943
3:169822227:C:A	S102R	0.943
3:169822227:C:G	S102R	0.943

dbSNP variants (sampled 300 via entrez): RS1000060204 (3:169835777 T>A), RS1000147880 (3:169831093 A>G), RS1000215370 (3:169824845 T>A), RS1000308179 (3:169829521 C>T), RS1000325840 (3:169819012 C>G), RS1000639077 (3:169828082 A>C,G), RS1000643104 (3:169826458 T>C,G), RS1000663394 (3:169820308 T>C), RS1000868814 (3:169835811 C>T), RS1000915757 (3:169813918 T>C), RS1000953311 (3:169826285 G>A,C), RS1001263042 (3:169813650 T>A), RS1001282984 (3:169831949 G>A,T), RS1001545137 (3:169819360 A>T), RS1001597673 (3:169819656 C>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
GCST004710_3	Renal cell carcinoma	9.000000e-09

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
abrine	increases expression	1
Arsenic	affects methylation	1
Vehicle Emissions	decreases methylation	1
Benzo(a)pyrene	affects methylation, increases methylation	1

Clinical trials (associated diseases)

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