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

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 (8 variants)
• Ciliary dyskinesia, primary, 39 (1 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.

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			3	80	7	90
missense		1	121	14	10	146
nonsense	3	1				4
start loss						0
frameshift	5					5
inframe indel			3			3
splice donor/acceptor (+/-2bp)		3				3
splice region			6	7	2	15
non coding				43	21	64
Total	8	5	127	137	38

Highest pathogenic variant AF is 0.0000263

Variants in LRRC56

This is a list of pathogenic ClinVar variants found in the LRRC56 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-540584-G-A			Benign (May 13, 2021)
11-540604-A-C			Benign (May 13, 2021)
11-540709-C-A			Uncertain significance (Jan 18, 2024)
11-540710-G-A			Uncertain significance (May 30, 2022)
11-540718-C-T		not specified	Uncertain significance (Sep 22, 2023)
11-540719-G-A		Ciliary dyskinesia, primary, 39 • LRRC56-related disorder	Benign (Jan 29, 2024)
11-540722-G-A			Uncertain significance (Mar 13, 2022)
11-540736-G-A		not specified	Conflicting classifications of pathogenicity (Dec 27, 2022)
11-540736-G-T			Uncertain significance (May 25, 2022)
11-540736-GTCC-G		Ciliary dyskinesia, primary, 39	Uncertain significance (Jun 02, 2023)
11-540739-C-A			Likely benign (Apr 25, 2022)
11-540739-C-T		not specified	Uncertain significance (Feb 03, 2022)
11-540740-G-A		LRRC56-related disorder	Benign (Jan 31, 2024)
11-540755-G-A			Uncertain significance (Apr 18, 2022)
11-540756-C-T			Likely benign (Sep 28, 2022)
11-540764-G-T			Uncertain significance (Aug 09, 2022)
11-540766-C-G			Uncertain significance (Nov 22, 2021)
11-540766-C-T			Likely benign (Jul 11, 2022)
11-540768-G-T			Likely benign (Jan 10, 2023)
11-540777-C-T			Likely benign (Dec 28, 2023)
11-540781-C-G			Uncertain significance (Jan 16, 2022)
11-540782-C-T		not specified	Uncertain significance (Jan 06, 2023)
11-540783-A-T			Likely benign (May 25, 2021)
11-540788-G-A		not specified	Uncertain significance (Jan 02, 2024)
11-540789-C-T			Likely benign (Dec 04, 2023)

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