LRRCC1

leucine rich repeat and coiled-coil centrosomal protein 1

Basic information

Region (hg38): 8:85107214-85146080

Links

ENSG00000133739 ∙ NCBI:85444 ∙ OMIM:617791 ∙ HGNC:29373 ∙ Uniprot:Q9C099 ∙ 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 LRRCC1 gene.

• Joubert syndrome and related disorders (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRCC1 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			1	12	3	16
missense	1		58	8	11	78
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region			1	1	3	5
non coding				2	4	6
Total	1	0	61	22	18

Variants in LRRCC1

This is a list of pathogenic ClinVar variants found in the LRRCC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-85107306-C-T		not specified	Uncertain significance (Aug 13, 2021)
8-85107309-C-A			Benign (Dec 11, 2023)
8-85107312-C-CGGT			Uncertain significance (Mar 18, 2022)
8-85107341-A-G			Uncertain significance (Aug 22, 2023)
8-85107355-C-T			Likely benign (Dec 28, 2023)
8-85107362-T-A		not specified	Uncertain significance (Jan 07, 2022)
8-85109592-T-C			Uncertain significance (Feb 14, 2022)
8-85109594-G-C		Joubert syndrome and related disorders	Pathogenic (Mar 29, 2024)
8-85109629-G-T		not specified	Uncertain significance (Dec 07, 2021)
8-85109674-G-T			Likely benign (Jan 15, 2024)
8-85109678-A-G			Uncertain significance (Oct 13, 2023)
8-85109680-A-G		not specified	Likely benign (May 18, 2023)
8-85109697-T-A			Benign (Jan 29, 2024)
8-85109735-G-A		not specified	Uncertain significance (Feb 17, 2022)
8-85109742-C-G		not specified	Uncertain significance (Feb 21, 2024)
8-85109746-C-G		not specified	Uncertain significance (May 26, 2024)
8-85109747-T-C		not specified	Uncertain significance (May 07, 2024)
8-85109759-G-A			Benign (Jan 24, 2024)
8-85109774-C-G		not specified	Uncertain significance (Mar 24, 2023)
8-85110101-CT-C			Benign (Jul 10, 2023)
8-85110105-T-G			Likely benign (Jun 13, 2022)
8-85112941-C-T		not specified	Uncertain significance (May 29, 2024)
8-85112947-A-G		not specified	Uncertain significance (Jul 13, 2021)
8-85112964-C-T			Uncertain significance (Feb 09, 2022)
8-85112982-C-T		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRCC1	protein_coding	protein_coding	ENST00000360375	19	38930

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.23e-21	0.296	124655	1	130	124786	0.000525

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.109	487	494	0.986	0.0000237	6858
Missense in Polyphen		72	98.197	0.73322		1494
Synonymous	0.226	168	172	0.978	0.00000881	1757
Loss of Function	1.76	39	52.8	0.739	0.00000262	717

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00174	0.00171
Ashkenazi Jewish	0.000105	0.0000993
East Asian	0.000692	0.000668
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000539	0.000521
Middle Eastern	0.000692	0.000668
South Asian	0.000431	0.000392
Other	0.000862	0.000825

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for the organization of the mitotic spindle. Maintains the structural integrity of centrosomes during mitosis. {ECO:0000269|PubMed:18728398}.

Recessive Scores

• pRec: 0.0964

Intolerance Scores

• loftool: 0.964
• rvis_EVS: 1.89
• rvis_percentile_EVS: 97.33

Haploinsufficiency Scores

• pHI: 0.172
• hipred: N
• hipred_score: 0.167
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00472

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrcc1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); reproductive system phenotype

Gene ontology

• Biological process: cell cycle;cell division
• Cellular component: cytoplasm;centrosome;centriole