LRRIQ1

Summary

LRRIQ1 (leucine rich repeats and IQ motif containing 1, HGNC:25708) is a protein-coding gene on chromosome 12q21.31, encoding Leucine-rich repeat- and IQ domain-containing protein 1 (Q96JM4).

Predicted to be involved in regulation of signal transduction. Predicted to be active in microtubule cytoskeleton.

Source: NCBI Gene 84125 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 289 total
• MANE Select transcript: NM_001079910

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25708
Approved symbol	LRRIQ1
Name	leucine rich repeats and IQ motif containing 1
Location	12q21.31
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12303, KIAA1801
Ensembl gene	ENSG00000133640
Ensembl biotype	protein_coding
OMIM	620922
Entrez	84125

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000393212, ENST00000393217, ENST00000525971, ENST00000526363, ENST00000528777, ENST00000529408, ENST00000533414, ENST00000602731

RefSeq mRNA: 1 — MANE Select: NM_001079910 NM_001079910

CCDS: CCDS41816

Canonical transcript exons

ENST00000393217 — 27 exons

Exon	Start	End
ENSE00001611552	85154012	85154094
ENSE00001735260	85153024	85153145
ENSE00001736255	85153663	85153758
ENSE00001753843	85152280	85152369
ENSE00001756082	85137850	85137969
ENSE00001799797	85127832	85128033
ENSE00002161291	85244789	85245105
ENSE00002222812	85036351	85036407
ENSE00002712689	85124070	85124519
ENSE00003469147	85046020	85046137
ENSE00003481828	85232696	85232756
ENSE00003528337	85104004	85104077
ENSE00003545288	85098867	85098994
ENSE00003549721	85038153	85038308
ENSE00003558719	85047247	85047470
ENSE00003567520	85121697	85121876
ENSE00003585248	85055547	85057184
ENSE00003611821	85044718	85044809
ENSE00003632170	85106522	85106615
ENSE00003643883	85066748	85066898
ENSE00003654374	85052177	85052251
ENSE00003658422	85072907	85073098
ENSE00003665537	85040490	85040601
ENSE00003671917	85065262	85065414
ENSE00003685044	85229517	85229649
ENSE00003693061	85098355	85098548
ENSE00003697215	85160613	85160714

Expression profiles

Bgee: expression breadth ubiquitous, 154 present calls, max score 93.59.

FANTOM5 (CAGE): breadth broad, TPM avg 2.2062 / max 323.2787, expressed in 531 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
127175	2.2062	531

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	93.59	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	92.07	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.93	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.60	gold quality
left testis	UBERON:0004533	82.12	gold quality
right testis	UBERON:0004534	81.98	gold quality
bronchial epithelial cell	CL:0002328	81.38	gold quality
testis	UBERON:0000473	80.13	gold quality
bronchus	UBERON:0002185	79.55	gold quality
ventricular zone	UBERON:0003053	76.80	gold quality
cortical plate	UBERON:0005343	73.08	gold quality
ganglionic eminence	UBERON:0004023	72.23	gold quality
adenohypophysis	UBERON:0002196	71.86	gold quality
metanephros cortex	UBERON:0010533	69.79	gold quality
pituitary gland	UBERON:0000007	69.33	gold quality
right lung	UBERON:0002167	68.86	gold quality
mucosa of paranasal sinus	UBERON:0005030	68.67	gold quality
hypothalamus	UBERON:0001898	68.15	gold quality
fallopian tube	UBERON:0003889	67.89	gold quality
caudate nucleus	UBERON:0001873	67.52	gold quality
nucleus accumbens	UBERON:0001882	66.67	gold quality
sural nerve	UBERON:0015488	66.24	gold quality
left lobe of thyroid gland	UBERON:0001120	65.96	gold quality
pancreatic ductal cell	CL:0002079	65.85	silver quality
thyroid gland	UBERON:0002046	65.80	gold quality
nasal cavity mucosa	UBERON:0001826	64.81	gold quality
right lobe of thyroid gland	UBERON:0001119	63.99	gold quality
islet of Langerhans	UBERON:0000006	63.89	gold quality
cortex of kidney	UBERON:0001225	62.72	gold quality
adult mammalian kidney	UBERON:0000082	62.17	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 8.

Experiment	Marker?	Max mean expression
E-ANND-2	yes	2611.96
E-MTAB-10287	yes	768.54
E-CURD-114	yes	718.53
E-CURD-122	yes	704.77
E-HCAD-1	yes	32.52
E-GEOD-130148	yes	13.54
E-MTAB-9388	yes	7.59
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lrriq1	ENSMUSG00000019892

Protein

Protein identifiers

Leucine-rich repeat- and IQ domain-containing protein 1 — Q96JM4 (reviewed: Q96JM4)

All UniProt accessions (6): A0A140VJN5, A0A3B3IS25, A8MY60, Q96JM4, H0YCJ9, H0YEZ5

UniProt curated annotations — full annotation on UniProt →

Isoforms (2)

UniProt ID	Names	Canonical?
Q96JM4-4	1	yes
Q96JM4-2	2

RefSeq proteins (1): NP_001073379* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000048	IQ_motif_EF-hand-BS	Binding_site
IPR001611	Leu-rich_rpt	Repeat
IPR003591	Leu-rich_rpt_typical-subtyp	Repeat
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR050836	SDS22/Internalin_LRR	Family

Pfam: PF00612, PF13855

UniProt features (27 total): repeat 10, region of interest 5, domain 4, compositionally biased region 3, sequence variant 3, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96JM4-F1	53.69	0.08

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 42 (showing top): GOBP_SINGLE_FERTILIZATION, chr12q21, GOBP_FERTILIZATION, HMG20B_TARGET_GENES, HMGA1_TARGET_GENES, OVOL3_TARGET_GENES, ZNF22_TARGET_GENES, ZNF407_TARGET_GENES, MIR6083, MIR583, MIR4640_3P, MEBARKI_HCC_PROGENITOR_FZD8CRD_UP, FAN_EMBRYONIC_CTX_EX_4_EXCITATORY_NEURON, MANNO_MIDBRAIN_NEUROTYPES_HRGL2A, MANNO_MIDBRAIN_NEUROTYPES_HRGL3

GO Biological Process (5): apoptotic process (GO:0006915), single fertilization (GO:0007338), regulation of signal transduction (GO:0009966), gene expression (GO:0010467), ectopic germ cell programmed cell death (GO:0035234)

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

GO Cellular Component (1): microtubule cytoskeleton (GO:0015630)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
fertilization	1
signal transduction	1
regulation of cell communication	1
regulation of signaling	1
regulation of response to stimulus	1
macromolecule biosynthetic process	1
developmental process involved in reproduction	1
programmed cell death involved in cell development	1
binding	1
cytoskeleton	1

Protein interactions and networks

STRING

999 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRIQ1	FAM120A2P	Q5T035	571
LRRIQ1	TSPAN19	P0C672	529
LRRIQ1	CFAP263	Q9H0I3	491
LRRIQ1	FEM1B	Q9UK73	461
LRRIQ1	ITPRID1	Q6ZRS4	461
LRRIQ1	ALX1	Q15699	450
LRRIQ1	OR1J4	Q8NGS1	448
LRRIQ1	CFAP52	Q8N1V2	437
LRRIQ1	ZNF227	Q86WZ6	431
LRRIQ1	CFAP70	Q5T0N1	410
LRRIQ1	FANK1	Q8TC84	405
LRRIQ1	NTS	P30990	398
LRRIQ1	CCT8L2	Q96SF2	395
LRRIQ1	RFNG	Q9Y644	391
LRRIQ1	LMO2	P25791	387

IntAct

4 interactions, top by confidence:

A	B	Type	Score
LRRIQ1	TNFRSF10B	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350
LRRIQ1	HES4	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (71): FGFR4 (Affinity Capture-MS), BMPR2 (Affinity Capture-MS), ACVR1 (Affinity Capture-MS), UNC5B (Affinity Capture-MS), FGFR2 (Affinity Capture-MS), ACVR2B (Affinity Capture-MS), PTPRS (Affinity Capture-MS), ACVR2A (Affinity Capture-MS), GTF2IRD1 (Affinity Capture-MS), BMPR1A (Affinity Capture-MS), EPHA3 (Affinity Capture-MS), NDFIP1 (Affinity Capture-MS), FYN (Affinity Capture-MS), STX10 (Affinity Capture-MS), NOTCH3 (Affinity Capture-MS)

ESM2 similar proteins: A0A0M3U1B0, A0A1L8EYB2, A0JP43, A1L2Y1, A2ARZ3, A4FU69, A4L9P8, A5WUN7, A7MC64, D3Z6S9, D3Z8E6, F5H4B4, Q06190, Q08AD1, Q0P5X1, Q0P5X5, Q16533, Q2T9M9, Q3V036, Q3ZAV0, Q497N6, Q4R6W9, Q53TS8, Q5CZC0, Q5MY90, Q5RHB5, Q5T4T6, Q5T5Y3, Q66H16, Q6NXP0, Q6Q759, Q6ZQ06, Q6ZVD7, Q86WZ0, Q8BQ48, Q8BYM7, Q8C4J0, Q8C636, Q8IWA6, Q8IYM0

Diamond homologs: Q0P5X1, Q4P5F9, Q96JM4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	247
Likely benign	21
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

5143 predictions. Top by Δscore:

Variant	Effect	Δscore
12:85038149:GCA:G	acceptor_gain	1.0000
12:85038168:T:G	acceptor_gain	1.0000
12:85038168:T:TA	acceptor_gain	1.0000
12:85038305:TACA:T	donor_gain	1.0000
12:85038306:ACA:A	donor_gain	1.0000
12:85038307:CA:C	donor_gain	1.0000
12:85038308:AG:A	donor_loss	1.0000
12:85038309:G:GG	donor_gain	1.0000
12:85038311:GAGTA:G	donor_loss	1.0000
12:85040481:A:G	acceptor_gain	1.0000
12:85040485:TTTA:T	acceptor_loss	1.0000
12:85040486:TTA:T	acceptor_loss	1.0000
12:85040488:A:AG	acceptor_gain	1.0000
12:85040488:A:AT	acceptor_loss	1.0000
12:85040489:G:GG	acceptor_gain	1.0000
12:85040597:TTTAA:T	donor_gain	1.0000
12:85040598:TTAA:T	donor_gain	1.0000
12:85040599:TAA:T	donor_gain	1.0000
12:85040600:AA:A	donor_gain	1.0000
12:85040602:G:GG	donor_gain	1.0000
12:85044713:TCTA:T	acceptor_loss	1.0000
12:85044715:TA:T	acceptor_loss	1.0000
12:85044716:A:AG	acceptor_gain	1.0000
12:85044717:G:GG	acceptor_gain	1.0000
12:85044717:GGCT:G	acceptor_gain	1.0000
12:85044805:TTAAG:T	donor_loss	1.0000
12:85044806:TAAGG:T	donor_loss	1.0000
12:85044807:AAGG:A	donor_loss	1.0000
12:85044808:AGG:A	donor_loss	1.0000
12:85044809:GGTAT:G	donor_loss	1.0000

AlphaMissense

11496 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:85098536:T:A	N1023K	0.996
12:85098536:T:G	N1023K	0.996
12:85098470:T:A	N1001K	0.995
12:85098470:T:G	N1001K	0.995
12:85104067:T:A	N1091K	0.995
12:85104067:T:G	N1091K	0.995
12:85098920:C:A	N1045K	0.994
12:85098920:C:G	N1045K	0.994
12:85106589:C:A	N1117K	0.992
12:85106589:C:G	N1117K	0.992
12:85066753:C:A	N850K	0.991
12:85066753:C:G	N850K	0.991
12:85066816:T:A	N871K	0.991
12:85066816:T:G	N871K	0.991
12:85066881:A:T	N893I	0.991
12:85098388:T:C	L974P	0.991
12:85098409:T:C	L981S	0.991
12:85098469:A:T	N1001I	0.991
12:85098992:C:A	N1069K	0.991
12:85098992:C:G	N1069K	0.991
12:85104051:T:C	L1086P	0.991
12:85098404:T:A	N979K	0.990
12:85098404:T:G	N979K	0.990
12:85098454:T:C	L996P	0.990
12:85098403:A:T	N979I	0.989
12:85066882:T:A	N893K	0.988
12:85066882:T:G	N893K	0.988
12:85098535:A:T	N1023I	0.988
12:85153757:T:A	W1546R	0.988
12:85153757:T:C	W1546R	0.988

dbSNP variants (sampled 300 via entrez): RS1000000145 (12:85178561 G>A), RS1000012926 (12:85055223 T>C), RS1000013502 (12:85228317 T>A), RS1000018097 (12:85105915 G>A,C), RS1000019008 (12:85149703 G>A), RS1000022955 (12:85039799 A>T), RS1000025068 (12:85047048 T>C), RS1000036598 (12:85046828 A>G), RS1000064621 (12:85134617 G>A,T), RS1000081142 (12:85234439 A>G), RS1000081320 (12:85091779 A>T), RS1000089790 (12:85041652 T>C), RS1000090568 (12:85149376 C>T), RS1000093558 (12:85036595 T>C), RS1000093951 (12:85134339 C>T)

Disease associations

OMIM: gene MIM:620922 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST003654_16	Bone mineral density (Ward’s triangle area)	4.000000e-06
GCST003996_8	Monobrow	1.000000e-12
GCST009462_73	Optic disc size	1.000000e-08
GCST010703_58	Brain morphology (MOSTest)	2.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0007785	femoral neck bone mineral density
EFO:0007906	synophrys measurement
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
butyraldehyde	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression, affects cotreatment, affects response to substance	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Catechin	affects cotreatment, decreases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Lipopolysaccharides	affects response to substance, increases expression, affects cotreatment	1
Methyl Methanesulfonate	increases expression	1
N-Nitrosopyrrolidine	decreases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	affects expression	1
Aflatoxin B1	decreases methylation	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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