LRRC70

leucine rich repeat containing 70

Basic information

Region (hg38): 5:62578819-62581446

Links

ENSG00000186105 ∙ NCBI:100130733 ∙ ∙ HGNC:35155 ∙ Uniprot:Q7Z2Q7 ∙ 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 LRRC70 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC70 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			38	1		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	1	0

Variants in LRRC70

This is a list of pathogenic ClinVar variants found in the LRRC70 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-62579451-C-A		not specified	Uncertain significance (Jan 05, 2022)
5-62579458-C-T		not specified	Uncertain significance (Feb 11, 2022)
5-62579549-G-C		not specified	Uncertain significance (Dec 26, 2023)
5-62579596-G-T		not specified	Uncertain significance (Nov 15, 2023)
5-62579623-C-T		not specified	Uncertain significance (Mar 07, 2024)
5-62579680-C-G		not specified	Uncertain significance (Jan 24, 2023)
5-62579692-C-T		not specified	Uncertain significance (May 05, 2023)
5-62579726-T-G		not specified	Uncertain significance (Dec 08, 2023)
5-62579802-C-T		not specified	Uncertain significance (Jun 13, 2022)
5-62579814-G-C		not specified	Uncertain significance (Nov 02, 2023)
5-62579881-C-T		not specified	Uncertain significance (Jan 08, 2024)
5-62579938-G-A		not specified	Uncertain significance (Jan 23, 2023)
5-62580057-G-C		not specified	Uncertain significance (Jan 06, 2023)
5-62580072-G-A		not specified	Uncertain significance (May 23, 2023)
5-62580076-G-C		not specified	Uncertain significance (Apr 12, 2022)
5-62580102-A-G		not specified	Uncertain significance (Jun 29, 2022)
5-62580123-A-C		not specified	Uncertain significance (May 10, 2023)
5-62580171-C-T		not specified	Uncertain significance (Jun 17, 2024)
5-62580226-G-C		not specified	Uncertain significance (Sep 17, 2021)
5-62580277-A-G		not specified	Uncertain significance (Dec 21, 2022)
5-62580290-T-G		not specified	Uncertain significance (Apr 27, 2023)
5-62580292-A-G		not specified	Uncertain significance (Jul 12, 2023)
5-62580339-A-G		not specified	Uncertain significance (Jun 03, 2022)
5-62580355-A-C		not specified	Uncertain significance (Aug 26, 2022)
5-62580411-G-T		not specified	Uncertain significance (Jan 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC70	protein_coding	protein_coding	ENST00000334994	1	2714

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.97e-7	0.689	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.52	176	299	0.589	0.0000144	4049
Missense in Polyphen		27	57.602	0.46873		916
Synonymous	1.98	86	113	0.762	0.00000534	1249
Loss of Function	1.20	13	18.6	0.699	0.00000108	270

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

• Function: FUNCTION: Renders cells highly sensitive to the activation by cytokines and lipopolysaccharide (LPS). {ECO:0000269|PubMed:12767927}.

Intolerance Scores

• rvis_EVS: 0.77
• rvis_percentile_EVS: 86.89

Haploinsufficiency Scores

• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Cellular component: integral component of membrane