LRRC69

leucine rich repeat containing 69, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 8:91101832-91219257

Links

ENSG00000214954 ∙ NCBI:100130742 ∙ ∙ HGNC:34303 ∙ Uniprot:Q6ZNQ3 ∙ 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 LRRC69 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC69 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				2		2
missense			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	3	0

Variants in LRRC69

This is a list of pathogenic ClinVar variants found in the LRRC69 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-91102695-G-C		not specified	Uncertain significance (Jun 24, 2022)
8-91102701-A-G		not specified	Uncertain significance (May 07, 2024)
8-91102708-C-T		not specified	Uncertain significance (Apr 01, 2024)
8-91102723-T-C		not specified	Uncertain significance (Aug 20, 2023)
8-91124578-T-C		not specified	Uncertain significance (Mar 27, 2023)
8-91124584-G-A		not specified	Uncertain significance (Aug 20, 2023)
8-91124596-G-A		not specified	Uncertain significance (Mar 22, 2022)
8-91127095-A-T		not specified	Uncertain significance (Jun 05, 2023)
8-91127127-A-G		not specified	Uncertain significance (Jul 20, 2021)
8-91127132-C-T		not specified	Uncertain significance (Aug 16, 2022)
8-91127145-C-T		not specified	Uncertain significance (May 24, 2024)
8-91133227-C-T			Likely benign (Apr 01, 2023)
8-91133234-G-A		not specified	Uncertain significance (Aug 15, 2023)
8-91133301-C-T		not specified	Uncertain significance (Nov 07, 2022)
8-91135695-A-C		not specified	Uncertain significance (Apr 19, 2023)
8-91135699-T-G		not specified	Uncertain significance (Oct 10, 2023)
8-91189566-A-C			Likely benign (Apr 01, 2023)
8-91189570-T-A		not specified	Uncertain significance (Dec 07, 2021)
8-91189609-G-A		not specified	Likely benign (Jan 03, 2022)
8-91200636-G-C		not specified	Uncertain significance (Jun 29, 2022)
8-91200637-A-C		not specified	Uncertain significance (Feb 10, 2023)
8-91200725-G-A		not specified	Uncertain significance (Dec 09, 2023)
8-91200731-T-C		not specified	Uncertain significance (May 31, 2024)
8-91200745-T-C		not specified	Uncertain significance (Aug 02, 2023)
8-91218920-G-A		not specified	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC69	protein_coding	protein_coding	ENST00000448384	8	117405

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000112	0.599	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.604	111	130	0.851	0.00000626	2262
Missense in Polyphen		25	31.638	0.7902		552
Synonymous	0.753	43	49.8	0.864	0.00000252	653
Loss of Function	0.830	9	12.1	0.743	5.57e-7	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.356

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc69