LRRC71

leucine rich repeat containing 71

Basic information

Region (hg38): 1:156920632-156933094

Previous symbols: [ "C1orf92" ]

Links

ENSG00000160838 ∙ NCBI:149499 ∙ ∙ HGNC:26556 ∙ Uniprot:Q8N4P6 ∙ 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 LRRC71 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC71 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			28	3		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	3	0

Variants in LRRC71

This is a list of pathogenic ClinVar variants found in the LRRC71 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-156920859-C-A		not specified	Uncertain significance (Jul 25, 2023)
1-156920922-C-T		not specified	Uncertain significance (Jul 06, 2021)
1-156923963-T-A		not specified	Likely benign (Dec 14, 2023)
1-156923967-G-C		not specified	Uncertain significance (May 02, 2024)
1-156923993-C-T		not specified	Uncertain significance (Aug 17, 2021)
1-156924000-C-A		not specified	Uncertain significance (Jun 07, 2024)
1-156924042-C-G		not specified	Uncertain significance (Oct 26, 2022)
1-156924068-T-C		not specified	Uncertain significance (May 24, 2024)
1-156924466-A-G		not specified	Uncertain significance (May 04, 2022)
1-156924672-G-A		not specified	Likely benign (Dec 14, 2023)
1-156924963-A-G		not specified	Uncertain significance (Apr 13, 2022)
1-156924999-T-C		not specified	Uncertain significance (May 26, 2022)
1-156927205-G-C		not specified	Uncertain significance (Apr 10, 2023)
1-156927213-T-A		not specified	Uncertain significance (Apr 07, 2022)
1-156927219-G-A		not specified	Uncertain significance (Feb 16, 2023)
1-156927255-T-G		not specified	Uncertain significance (Oct 26, 2022)
1-156927501-C-A		not specified	Uncertain significance (Jul 14, 2023)
1-156927555-G-A		not specified	Uncertain significance (May 08, 2023)
1-156927748-C-G		not specified	Uncertain significance (Feb 06, 2024)
1-156927790-G-C		not specified	Uncertain significance (Nov 23, 2022)
1-156927940-A-G		not specified	Uncertain significance (Mar 08, 2024)
1-156927948-G-A		not specified	Uncertain significance (Mar 31, 2024)
1-156929287-C-T		not specified	Uncertain significance (Apr 07, 2023)
1-156929311-C-T		not specified	Uncertain significance (Mar 25, 2024)
1-156929377-C-T		not specified	Likely benign (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC71	protein_coding	protein_coding	ENST00000337428	15	12445

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000191	0.994	124611	0	55	124666	0.000221

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.650	262	293	0.893	0.0000143	3517
Missense in Polyphen		76	82.112	0.92556		1041
Synonymous	0.866	115	127	0.902	0.00000656	1109
Loss of Function	2.46	14	28.1	0.498	0.00000143	334

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00140	0.00130
Ashkenazi Jewish	0.00	0.00
East Asian	0.000137	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000213	0.000203
Middle Eastern	0.000137	0.000111
South Asian	0.000105	0.0000980
Other	0.000191	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 1.04
• rvis_percentile_EVS: 91.29

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.380
• ghis: 0.415

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	High	Medium	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Lrrc71
• Phenotype: immune system phenotype; hematopoietic system phenotype