LRGUK

leucine rich repeats and guanylate kinase domain containing, the group of Cilia and flagella associated

Basic information

Region (hg38): 7:134127299-134264595

Links

ENSG00000155530 ∙ NCBI:136332 ∙ OMIM:616478 ∙ HGNC:21964 ∙ Uniprot:Q96M69 ∙ 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 LRGUK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRGUK 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						0
missense			51	3		54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	51	3	0

Variants in LRGUK

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

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

Position	Type	Phenotype	Significance	ClinVar
7-134127396-G-A		not specified	Uncertain significance (Apr 17, 2024)
7-134127403-A-C		not specified	Uncertain significance (Mar 20, 2023)
7-134127404-G-A		not specified	Uncertain significance (Sep 01, 2021)
7-134127435-C-A		not specified	Uncertain significance (Jun 02, 2023)
7-134127437-C-G		not specified	Uncertain significance (Sep 30, 2021)
7-134127510-A-G		not specified	Uncertain significance (Oct 16, 2023)
7-134127570-G-A		not specified	Uncertain significance (Oct 25, 2022)
7-134127611-G-A		not specified	Uncertain significance (Nov 09, 2021)
7-134137083-C-T		not specified	Uncertain significance (Dec 14, 2023)
7-134148242-C-T		not specified	Likely benign (Dec 12, 2022)
7-134148287-C-A		not specified	Uncertain significance (Mar 18, 2024)
7-134158113-C-T		not specified	Likely benign (Jun 11, 2024)
7-134158142-A-G		not specified	Uncertain significance (Feb 13, 2024)
7-134174575-T-C		not specified	Uncertain significance (Aug 14, 2023)
7-134174605-G-A		not specified	Uncertain significance (Jan 05, 2022)
7-134176992-T-C		not specified	Uncertain significance (Jul 14, 2021)
7-134177020-G-A		not specified	Uncertain significance (Feb 22, 2023)
7-134177041-A-G		not specified	Uncertain significance (Jun 07, 2024)
7-134178542-G-A		not specified	Uncertain significance (Jun 05, 2023)
7-134178555-A-G		not specified	Uncertain significance (Jul 14, 2021)
7-134178557-C-T		not specified	Uncertain significance (Jun 14, 2023)
7-134183766-T-C		not specified	Uncertain significance (Dec 27, 2022)
7-134183766-T-G		not specified	Uncertain significance (Feb 22, 2023)
7-134183802-G-A		not specified	Uncertain significance (Oct 10, 2023)
7-134183825-A-G		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRGUK	protein_coding	protein_coding	ENST00000285928	20	137292

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.45e-15	0.728	125653	0	95	125748	0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.327	460	441	1.04	0.0000221	5402
Missense in Polyphen		134	138.03	0.97083		1761
Synonymous	-0.268	169	165	1.03	0.00000877	1545
Loss of Function	1.88	30	43.3	0.693	0.00000215	549

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000897	0.000892
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.000273	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000381	0.000378
Middle Eastern	0.000273	0.000272
South Asian	0.000689	0.000686
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in multiple aspects of sperm assembly including acrosome attachment, shaping of the sperm head and in the early aspects of axoneme development. Not essential for primary cilium biogenesis. {ECO:0000250|UniProtKB:Q9D5S7}.

Recessive Scores

• pRec: 0.0745

Intolerance Scores

• rvis_EVS: 1.81
• rvis_percentile_EVS: 96.96

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.266

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.110

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrguk
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype; cellular phenotype

Gene ontology

• Biological process: spermatogenesis;phosphorylation;cell differentiation;axoneme assembly;GMP metabolic process;GDP metabolic process
• Cellular component: acrosomal vesicle;manchette;cytosol;cell projection
• Molecular function: guanylate kinase activity;ATP binding