LRRC10B

leucine rich repeat containing 10B

Basic information

Region (hg38): 11:61508749-61511018

Links

ENSG00000204950 ∙ NCBI:390205 ∙ ∙ HGNC:37215 ∙ Uniprot:A6NIK2 ∙ 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 LRRC10B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC10B 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in LRRC10B

This is a list of pathogenic ClinVar variants found in the LRRC10B region.

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

Position	Type	Phenotype	Significance	ClinVar
11-61509057-G-A		not specified	Uncertain significance (Jan 08, 2024)
11-61509077-G-C		not specified	Uncertain significance (Dec 13, 2022)
11-61509112-C-G		not specified	Uncertain significance (Dec 20, 2021)
11-61509122-G-T		not specified	Uncertain significance (Dec 07, 2021)
11-61509138-A-G		not specified	Uncertain significance (Oct 20, 2023)
11-61509226-C-A		not specified	Uncertain significance (Jul 26, 2022)
11-61509361-G-C		not specified	Uncertain significance (Nov 09, 2023)
11-61509375-G-A		not specified	Uncertain significance (May 07, 2024)
11-61509433-C-A		not specified	Uncertain significance (Apr 13, 2022)
11-61509506-C-A		not specified	Uncertain significance (Jan 05, 2022)
11-61509506-C-G		not specified	Uncertain significance (Jun 29, 2023)
11-61509620-G-C		not specified	Uncertain significance (Oct 25, 2023)
11-61509689-G-A		not specified	Uncertain significance (Jul 09, 2021)
11-61509704-C-A		not specified	Uncertain significance (Dec 17, 2023)
11-61509746-C-T		not specified	Uncertain significance (Jul 14, 2021)
11-61509774-A-G		not specified	Uncertain significance (Jul 20, 2022)
11-61509776-G-A		not specified	Uncertain significance (Apr 07, 2022)
11-61509779-G-A		not specified	Uncertain significance (Nov 07, 2023)
11-61509785-G-A		not specified	Uncertain significance (Jan 23, 2024)
11-61509851-G-A		not specified	Uncertain significance (Sep 01, 2021)
11-61509857-G-A		not specified	Uncertain significance (Feb 06, 2023)
11-61509869-G-A		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC10B	protein_coding	protein_coding	ENST00000378075	1	2211

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0449	0.686	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	72	109	0.660	0.00000575	1781
Missense in Polyphen		12	25.147	0.4772		470
Synonymous	1.81	39	56.2	0.694	0.00000307	688
Loss of Function	0.569	2	3.08	0.650	1.34e-7	49

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

Haploinsufficiency Scores

• ghis: 0.508

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

Mouse Genome Informatics

• Gene name: Lrrc10b