LRRC20

leucine rich repeat containing 20

Basic information

Region (hg38): 10:70298970-70382650

Links

ENSG00000172731 ∙ NCBI:55222 ∙ ∙ HGNC:23421 ∙ Uniprot:Q8TCA0 ∙ 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 LRRC20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC20 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in LRRC20

This is a list of pathogenic ClinVar variants found in the LRRC20 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-70301362-G-T		not specified	Uncertain significance (Dec 20, 2023)
10-70301367-G-A		not specified	Uncertain significance (Nov 06, 2023)
10-70301368-C-T		not specified	Uncertain significance (Nov 09, 2022)
10-70301412-G-A		not specified	Uncertain significance (Aug 23, 2021)
10-70301415-G-A		not specified	Uncertain significance (Nov 08, 2022)
10-70301419-C-T		not specified	Uncertain significance (Sep 27, 2021)
10-70301428-G-A		not specified	Uncertain significance (May 25, 2022)
10-70301437-C-T		not specified	Uncertain significance (Oct 24, 2023)
10-70301454-C-T		not specified	Uncertain significance (Nov 17, 2023)
10-70301455-G-A		not specified	Uncertain significance (May 17, 2023)
10-70301470-G-A		not specified	Uncertain significance (Dec 02, 2024)
10-70301500-C-T		not specified	Uncertain significance (Apr 25, 2023)
10-70323871-T-C		not specified	Uncertain significance (Aug 27, 2024)
10-70323872-C-T		not specified	Uncertain significance (Mar 06, 2023)
10-70323898-A-G		not specified	Uncertain significance (Feb 15, 2023)
10-70323927-G-C		not specified	Uncertain significance (Sep 25, 2023)
10-70323952-A-T		not specified	Uncertain significance (Nov 26, 2024)
10-70324004-G-A		not specified	Uncertain significance (Mar 24, 2023)
10-70324028-G-T		not specified	Uncertain significance (Jun 06, 2023)
10-70340555-C-T		not specified	Likely benign (Jan 04, 2024)
10-70340565-T-G		not specified	Uncertain significance (Oct 03, 2022)
10-70340639-G-C		not specified	Uncertain significance (Jun 10, 2024)
10-70340648-C-T		not specified	Uncertain significance (Jun 25, 2024)
10-70340694-C-T		not specified	Uncertain significance (Feb 27, 2024)
10-70376478-G-A		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC20	protein_coding	protein_coding	ENST00000355790	4	83654

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0439	0.859	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.465	110	125	0.883	0.00000825	1203
Missense in Polyphen		5	8.165	0.61237		102
Synonymous	-0.583	63	57.4	1.10	0.00000427	386
Loss of Function	1.36	3	6.83	0.440	3.76e-7	72

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.000595	0.000595
East Asian	0.000435	0.000435
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000308	0.000308
Middle Eastern	0.000435	0.000435
South Asian	0.0000653	0.0000653
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.325
• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

• pHI: 0.291
• hipred: N
• hipred_score: 0.458
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.714

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc20

Gene ontology

• Molecular function: protein binding