LRRC66

leucine rich repeat containing 66

Basic information

Region (hg38): 4:51993651-52020363

Links

ENSG00000188993 ∙ NCBI:339977 ∙ ∙ HGNC:34299 ∙ Uniprot:Q68CR7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LRRC66 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC66 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			48	8		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	8	0

Variants in LRRC66

This is a list of pathogenic ClinVar variants found in the LRRC66 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-51994413-G-A		not specified	Uncertain significance (May 14, 2024)
4-51994477-C-T		not specified	Likely benign (Jun 14, 2023)
4-51994647-T-C		not specified	Likely benign (Jun 24, 2022)
4-51994672-C-G		not specified	Uncertain significance (Dec 18, 2023)
4-51994681-G-A		not specified	Uncertain significance (Nov 22, 2021)
4-51994810-C-G		not specified	Uncertain significance (Feb 03, 2022)
4-51994852-T-C		not specified	Uncertain significance (Jan 16, 2024)
4-51994854-C-T		not specified	Likely benign (Aug 30, 2022)
4-51994855-T-G		not specified	Uncertain significance (Dec 08, 2023)
4-51994948-G-C		not specified	Uncertain significance (Apr 08, 2024)
4-51995028-C-T		not specified	Likely benign (Nov 06, 2023)
4-51995079-G-C		not specified	Uncertain significance (Jan 30, 2024)
4-51995088-G-C		not specified	Uncertain significance (Sep 07, 2022)
4-51995164-A-G		not specified	Uncertain significance (May 23, 2023)
4-51995168-C-T		not specified	Uncertain significance (Sep 01, 2021)
4-51995169-A-G		not specified	Uncertain significance (Mar 08, 2024)
4-51995198-GC-G		Abnormality of neuronal migration	Benign (Oct 31, 2014)
4-51995292-T-A		not specified	Uncertain significance (Jul 27, 2022)
4-51995293-C-A		not specified	Uncertain significance (Feb 21, 2024)
4-51995328-A-C		not specified	Uncertain significance (May 09, 2023)
4-51995333-G-C		not specified	Likely benign (Oct 06, 2022)
4-51995349-A-G		not specified	Uncertain significance (Oct 27, 2023)
4-51995370-T-A		not specified	Uncertain significance (May 24, 2024)
4-51995375-A-C		not specified	Uncertain significance (Aug 20, 2023)
4-51995389-C-T		not specified	Uncertain significance (Jun 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC66	protein_coding	protein_coding	ENST00000343457	4	23919

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.50e-10	0.0305	124753	0	24	124777	0.0000962

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.23	543	468	1.16	0.0000245	5805
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000153
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000567	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000144	0.000141
Middle Eastern	0.0000567	0.0000556
South Asian	0.0000664	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.688
• rvis_EVS: 0.43
• rvis_percentile_EVS: 77.29

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0350

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc66

Gene ontology

• Cellular component: integral component of membrane