LRRC56

leucine rich repeat containing 56, the group of Axonemal dynein assembly factors

Basic information

Region (hg38): 11:537527-554912

Links

ENSG00000161328 ∙ NCBI:115399 ∙ OMIM:618227 ∙ HGNC:25430 ∙ Uniprot:Q8IYG6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ciliary dyskinesia, primary, 39 (Strong), mode of inheritance: AR
• primary ciliary dyskinesia (Supportive), mode of inheritance: AD
• ciliary dyskinesia, primary, 39 (Limited), mode of inheritance: AR
• ciliary dyskinesia, primary, 39 (Strong), mode of inheritance: AR
• ciliary dyskinesia, primary, 39 (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliary dyskinesia, primary 39	AR	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Pulmonary	Pulmonary and audiologic surveillance may be beneficial to assess respiratory and hearing function and institute early management measures; In order to facilitate mucus clearance, aggressive interventions (eg, chest percussion and oscillatory vest), as well as vaccinations and early and aggressive treatment of respiratory infections may be beneficial; Individuals may require surgery or other interventions related to congenital cardiac malformations	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Gastrointestinal; Pulmonary	30388400

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LRRC56 gene.

• not_provided (304 variants)
• not_specified (108 variants)
• LRRC56-related_disorder (40 variants)
• Ciliary_dyskinesia,_primary,_39 (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC56 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000198075.4. 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			2	99	4	105
missense	1	1	160	16	10	188
nonsense	4	1				5
start loss						0
frameshift	7					7
splice donor/acceptor (+/-2bp)	2	4				6
Total	14	6	162	115	14

Highest pathogenic variant AF is 0.000139736

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC56	protein_coding	protein_coding	ENST00000270115	11	17390

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.68e-10	0.266	125483	0	36	125519	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.883	353	309	1.14	0.0000188	3371
Missense in Polyphen		83	75.751	1.0957		947
Synonymous	-3.38	188	138	1.37	0.00000825	1223
Loss of Function	0.739	16	19.5	0.820	8.35e-7	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000907	0.0000906
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000557	0.000555
European (Non-Finnish)	0.000155	0.000150
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000985	0.0000980
Other	0.000206	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.740
• rvis_EVS: 2.38
• rvis_percentile_EVS: 98.47

Haploinsufficiency Scores

• pHI: 0.117
• hipred: N
• hipred_score: 0.145
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.206

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc56