LRRCC1

leucine rich repeat and coiled-coil centrosomal protein 1

Basic information

Region (hg38): 8:85107215-85146080

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.

• not_specified (113 variants)
• not_provided (73 variants)
• Joubert_syndrome_and_related_disorders (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. These statistics are base on transcript: NM_000033402.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				16	2	18
missense			110	19	7	136
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)	1		2			3
Total	1	0	112	35	9

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