LRRC17

leucine rich repeat containing 17

Basic information

Region (hg38): 7:102913000-102945111

Links

ENSG00000128606 ∙ NCBI:10234 ∙ OMIM:618749 ∙ HGNC:16895 ∙ Uniprot:Q8N6Y2 ∙ 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 LRRC17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC17 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	21	1	0

Variants in LRRC17

This is a list of pathogenic ClinVar variants found in the LRRC17 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-102913214-G-T		not specified	Uncertain significance (Aug 12, 2021)
7-102926299-T-G		not specified	Uncertain significance (Jun 11, 2021)
7-102926335-C-T		not specified	Uncertain significance (Jun 29, 2023)
7-102926340-G-A		not specified	Uncertain significance (Sep 13, 2023)
7-102933983-G-T		not specified	Uncertain significance (Dec 19, 2022)
7-102934020-G-A		not specified	Uncertain significance (Aug 09, 2021)
7-102934025-G-A		not specified	Likely benign (Feb 10, 2022)
7-102934034-G-C		not specified	Uncertain significance (Mar 25, 2024)
7-102934094-C-T		not specified	Uncertain significance (Oct 13, 2023)
7-102934254-A-G		not specified	Uncertain significance (Dec 06, 2022)
7-102934389-G-A		not specified	Uncertain significance (Dec 19, 2023)
7-102934411-C-G		not specified	Uncertain significance (Dec 20, 2023)
7-102934523-C-G		not specified	Uncertain significance (Nov 21, 2023)
7-102934523-C-T		not specified	Uncertain significance (Feb 07, 2023)
7-102934524-G-A		not specified	Uncertain significance (May 27, 2022)
7-102934596-G-A		not specified	Uncertain significance (Aug 08, 2022)
7-102934602-C-G		not specified	Uncertain significance (Feb 16, 2023)
7-102934602-C-T		not specified	Uncertain significance (Jun 18, 2021)
7-102939453-A-T		not specified	Uncertain significance (Jan 03, 2022)
7-102939499-A-C		not specified	Uncertain significance (Jun 22, 2023)
7-102944212-G-A		not specified	Uncertain significance (May 02, 2024)
7-102944411-A-C		not specified	Uncertain significance (Jul 21, 2021)
7-102944450-G-A		not specified	Uncertain significance (Oct 04, 2022)
7-102944501-C-T		not specified	Uncertain significance (Apr 23, 2024)
7-102944597-T-A		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC17	protein_coding	protein_coding	ENST00000339431	3	31959

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.15e-7	0.571	125700	0	48	125748	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.542	213	236	0.901	0.0000125	2911
Missense in Polyphen		58	75.042	0.7729		910
Synonymous	-0.538	102	95.3	1.07	0.00000532	793
Loss of Function	1.02	13	17.6	0.737	8.58e-7	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000524	0.000518
Ashkenazi Jewish	0.000199	0.0000992
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.000164	0.000163
South Asian	0.000163	0.000163
Other	0.000172	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in bone homeostasis. Acts as a negative regulator of RANKL-induced osteoclast precursor differentiation from bone marrow precursors (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.641
• rvis_EVS: 1.11
• rvis_percentile_EVS: 92.04

Haploinsufficiency Scores

• pHI: 0.454
• hipred: N
• hipred_score: 0.282
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.160

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc17
• Phenotype: immune system phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype

Gene ontology

• Biological process: osteoblast differentiation;osteoblast proliferation;negative regulation of osteoclast differentiation;bone marrow development
• Cellular component: extracellular space;extracellular matrix