LRRC66

protein-coding

leucine rich repeat containing 66

Gene summary

This gene encodes a protein belonging to the leucine-rich repeat family of proteins, which are involved in diverse biological processes, including cell adhesion, cellular trafficking, and hormone-receptor interactions. [provided by RefSeq, Apr 2017]

MANE transcript

NM_001024611.3

Inheritance

—

ClinVar variants

U:129B:13

Top phenotype

Abnormality of neuronal migration

gnomAD constraint

pLI —, LoF o/e 1.22

Max pathogenic AF

—

Genomic locus

chr4:51,993,652-52,020,363

External References & Databases

Ensembl (ENSG00000188993)

Transcript & Mutation Effects

hg38 • Region Span ~26.7 kb

Loading mutation effect viewer...

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 LRRC66 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 138

not providedTotal: 2

Abnormality of neuronal migrationTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001024611.3. 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						0
missense			127 clinvar	12 clinvar		139
nonsense						0
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	129	12	1	142

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001024611.3	RefSeq	NP_001019782.1	4	MANE Select
ENST00000682860.1	Ensembl	ENSP00000508002.1	4	MANE Select
ENST00000343457.3	Ensembl	ENSP00000341944.3	4	Standard
ENST00000343457.4	Ensembl	ENSP00000341944.3	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000343457
Coding exons: 4
Length: 23919
Individuals with no LoFs: 124753
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 124777
p: 0.0000962

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.23	543	468	1.16	0.0000245	5805
Missense (PolyPhen)		62	57.632	1.0758		832
Synonymous	-0.718	200	187	1.07	0.0000113	1722
Loss of Function	-0.663	13	10.7	1.22	4.47e-7	144

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000057	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.688
RVIS EVS: 0.43
RVIS percentile EVS: 77.29

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0350

Gene Damage Prediction

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