LRRC3B

leucine rich repeat containing 3B

Basic information

Region (hg38): 3:26622772-26717537

Links

ENSG00000179796 ∙ NCBI:116135 ∙ OMIM:618996 ∙ HGNC:28105 ∙ Uniprot:Q96PB8 ∙ 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 LRRC3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC3B 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					1	1
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	1

Variants in LRRC3B

This is a list of pathogenic ClinVar variants found in the LRRC3B region.

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

Position	Type	Phenotype	Significance	ClinVar
3-26709700-C-G		not specified	Uncertain significance (May 06, 2022)
3-26709728-A-G		not specified	Uncertain significance (Jun 06, 2023)
3-26709851-G-A		not specified	Uncertain significance (Aug 12, 2022)
3-26710245-C-T			Benign (Nov 14, 2018)
3-26710246-G-A		not specified	Uncertain significance (Sep 30, 2021)
3-26710314-C-A		not specified	Uncertain significance (Feb 12, 2024)
3-26710330-T-C		not specified	Uncertain significance (Jan 26, 2022)
3-26710336-G-T		not specified	Uncertain significance (Jan 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC3B	protein_coding	protein_coding	ENST00000396641	1	87971

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.444	0.530	125695	0	9	125704	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.10	75	147	0.511	0.00000763	1731
Missense in Polyphen		17	51.381	0.33086		641
Synonymous	0.0550	59	59.5	0.991	0.00000345	507
Loss of Function	1.78	1	5.49	0.182	2.30e-7	77

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.387
• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.68

Haploinsufficiency Scores

• pHI: 0.303
• hipred: Y
• hipred_score: 0.651
• ghis: 0.638

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.354

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc3b

Gene ontology

• Cellular component: extracellular space;integral component of membrane;extracellular matrix