LRRC3

leucine rich repeat containing 3

Basic information

Region (hg38): 21:44455510-44462196

Previous symbols: [ "C21orf102", "LRRC3DN", "C21orf30" ]

Links

ENSG00000160233 ∙ NCBI:81543 ∙ OMIM:617620 ∙ HGNC:14965 ∙ Uniprot:Q9BY71 ∙ 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 LRRC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC3 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	3		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	17	3	0

Variants in LRRC3

This is a list of pathogenic ClinVar variants found in the LRRC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-44456693-C-T		not specified	Uncertain significance (Jul 16, 2021)
21-44456711-C-T		not specified	Uncertain significance (Aug 02, 2023)
21-44456756-C-G		not specified	Uncertain significance (Jul 19, 2022)
21-44456774-G-A		not specified	Uncertain significance (Sep 17, 2021)
21-44456778-C-T		not specified	Uncertain significance (Dec 27, 2022)
21-44456780-G-T		not specified	Uncertain significance (May 13, 2024)
21-44456802-G-A		not specified	Uncertain significance (Jun 21, 2023)
21-44456822-G-A		not specified	Likely benign (Aug 08, 2022)
21-44456828-A-G		not specified	Uncertain significance (Apr 08, 2024)
21-44456832-C-T		not specified	Uncertain significance (Jun 27, 2022)
21-44456909-C-T		not specified	Uncertain significance (Feb 27, 2024)
21-44456951-A-T		not specified	Uncertain significance (Oct 20, 2023)
21-44456954-G-A		not specified	Uncertain significance (Aug 15, 2023)
21-44456982-G-A		not specified	Uncertain significance (Nov 08, 2022)
21-44456990-C-T		not specified	Uncertain significance (Dec 15, 2023)
21-44456991-G-A		not specified	Uncertain significance (May 24, 2024)
21-44457050-C-A		not specified	Uncertain significance (Sep 20, 2023)
21-44457066-G-A		not specified	Uncertain significance (Aug 21, 2023)
21-44457162-A-C		not specified	Uncertain significance (Mar 20, 2023)
21-44457207-C-G		not specified	Uncertain significance (Jun 01, 2023)
21-44457254-G-C		not specified	Uncertain significance (May 09, 2024)
21-44457302-G-A		not specified	Likely benign (Dec 28, 2023)
21-44457324-G-A		not specified	Uncertain significance (May 10, 2024)
21-44457344-C-T		not specified	Uncertain significance (Nov 21, 2022)
21-44457404-G-A		not specified	Likely benign (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC3	protein_coding	protein_coding	ENST00000291592	1	3371

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00270	0.581	125677	0	19	125696	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.258	169	179	0.946	0.0000123	1639
Missense in Polyphen		44	54.135	0.81278		567
Synonymous	-0.440	90	84.8	1.06	0.00000614	575
Loss of Function	0.349	4	4.83	0.829	2.07e-7	51

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000370	0.000369
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000555	0.0000544
Finnish	0.0000490	0.0000462
European (Non-Finnish)	0.0000982	0.0000968
Middle Eastern	0.0000555	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.309
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.36

Haploinsufficiency Scores

• pHI: 0.144
• hipred: N
• hipred_score: 0.231
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.229

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc3

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: protein binding