LRRIQ1

protein-coding

leucine rich repeats and IQ motif containing 1

Gene summary

Predicted to be involved in regulation of signal transduction. Predicted to act upstream of or within apoptotic process; gene expression; and single fertilization. Predicted to be active in microtubule cytoskeleton. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001079910.2

Inheritance

—

ClinVar variants

U:264B:22

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.77

Max pathogenic AF

—

Genomic locus

chr12:85,036,314-85,264,457

External References & Databases

Ensembl (ENSG00000133640)

Transcript & Mutation Effects

hg38 • Region Span ~228.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LRRIQ1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 269

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001079910.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			261 clinvar	21 clinvar		282
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	264	22	0	286

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001079910.2	RefSeq	NP_001073379.1	26	MANE Select
ENST00000393217.7	Ensembl	ENSP00000376910.2	26	MANE Select
ENST00000393212.7	Ensembl	ENSP00000376906.3	5	Standard
ENST00000526363.1	Ensembl	ENSP00000431756.1	3	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000393217
Coding exons: 26
Length: 226911
Individuals with no LoFs: 69458
Homozygous LoFs: 8739
Heterozygous LoFs: 47540
Defined: 125737
p: 0.257

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.09	882	796	1.11	0.0000377	11366
Missense (PolyPhen)		187	183.18	1.0209		2723
Synonymous	-0.953	298	278	1.07	0.0000131	2953
Loss of Function	2.04	68	88.7	0.767	0.00000462	1202

Population LoF Frequency

Population	CAF	p-value	Status
African	0.15	0.11	notable
Latino/Admixed American	0.34	0.29	notable
Ashkenazi Jewish	0.34	0.30	notable
East Asian	0.21	0.16	notable
Finnish	0.28	0.26	notable
European (Non-Finnish)	0.33	0.28	notable
South Asian	0.30	0.25	notable
Other	0.32	0.26	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.997
RVIS EVS: 0.8
RVIS percentile EVS: 87.41

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0426

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium