LRRC45

leucine rich repeat containing 45

Basic information

Region (hg38): 17:82023305-82031151

Links

ENSG00000169683 ∙ NCBI:201255 ∙ ∙ HGNC:28302 ∙ Uniprot:Q96CN5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ciliopathy (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LRRC45 gene.

• not_specified (111 variants)
• LRRC45-related_disorder (64 variants)
• not_provided (2 variants)
• LRRC45_associated_neurological_ciliopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC45 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000144999.4. 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			1	15		16
missense			116	13		129
nonsense			1			1
start loss						0
frameshift			2			2
splice donor/acceptor (+/-2bp)	1		1			2
Total	1	0	121	28	0

Highest pathogenic variant AF is 0.0000113217

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC45	protein_coding	protein_coding	ENST00000306688	17	7850

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.96e-11	0.956	125193	0	61	125254	0.000244

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	325	381	0.853	0.0000237	4253
Missense in Polyphen		80	85.117	0.93988		1017
Synonymous	0.400	160	167	0.961	0.0000101	1337
Loss of Function	2.15	23	37.2	0.619	0.00000185	409

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000639	0.000635
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000318	0.000310
Middle Eastern	0.0000544	0.0000544
South Asian	0.000331	0.000196
Other	0.000361	0.000327

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the proteinaceous fiber-like linker between two centrioles, required for centrosome cohesion. {ECO:0000269|PubMed:24035387}.

Intolerance Scores

• loftool: 0.781
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.65

Haploinsufficiency Scores

• pHI: 0.193
• hipred: N
• hipred_score: 0.289
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.469

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc45

Gene ontology

• Cellular component: nucleoplasm;centrosome;cytosol;plasma membrane
• Molecular function: protein binding