LRRC14B

leucine rich repeat containing 14B

Basic information

Region (hg38): 5:191494-196334

Links

ENSG00000185028 ∙ NCBI:389257 ∙ ∙ HGNC:37268 ∙ Uniprot:A6NHZ5 ∙ 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 LRRC14B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC14B 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			31	3	1	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	3	1

Variants in LRRC14B

This is a list of pathogenic ClinVar variants found in the LRRC14B region.

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

Position	Type	Phenotype	Significance	ClinVar
5-191550-G-A		not specified	Uncertain significance (May 24, 2023)
5-191560-C-T		not specified	Uncertain significance (Aug 10, 2021)
5-191618-A-G		not specified	Uncertain significance (Sep 16, 2021)
5-191633-A-G		not specified	Uncertain significance (Oct 29, 2021)
5-191689-C-T		not specified	Uncertain significance (Dec 15, 2022)
5-191755-G-A		not specified	Uncertain significance (Oct 13, 2023)
5-191773-C-T		not specified	Uncertain significance (Dec 12, 2023)
5-191863-G-A		not specified	Uncertain significance (Feb 27, 2023)
5-191970-G-C		not specified	Uncertain significance (Apr 22, 2024)
5-192004-G-A		not specified	Uncertain significance (Jan 08, 2024)
5-192007-G-A		not specified	Uncertain significance (Apr 13, 2023)
5-192037-G-A			Benign (Apr 01, 2024)
5-192113-G-C		not specified	Uncertain significance (Aug 14, 2023)
5-192155-G-A		not specified	Uncertain significance (Dec 08, 2022)
5-192178-C-T		not specified	Uncertain significance (Jun 28, 2023)
5-192202-G-A		not specified	Uncertain significance (Apr 08, 2024)
5-192215-C-T		not specified	Uncertain significance (Dec 27, 2022)
5-192230-A-G		not specified	Uncertain significance (Mar 17, 2023)
5-192298-C-A		not specified	Uncertain significance (Jan 22, 2024)
5-192407-C-G		not specified	Likely benign (Jan 08, 2024)
5-192415-G-A		not specified	Uncertain significance (Aug 14, 2023)
5-192425-C-G		not specified	Uncertain significance (Apr 17, 2024)
5-194710-C-G		not specified	Uncertain significance (Aug 16, 2021)
5-194722-C-T		not specified	Uncertain significance (Nov 30, 2022)
5-194764-C-T		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC14B	protein_coding	protein_coding	ENST00000328278	2	3843

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.06e-9	0.0500	124507	0	159	124666	0.000638

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.124	306	312	0.980	0.0000212	3205
Missense in Polyphen		90	82.576	1.0899		1033
Synonymous	-0.0128	152	152	1.00	0.0000108	1167
Loss of Function	-0.374	13	11.6	1.12	7.03e-7	111

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00137	0.00127
Ashkenazi Jewish	0.00380	0.00338
East Asian	0.000597	0.000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000568	0.000531
Middle Eastern	0.000597	0.000556
South Asian	0.000771	0.000752
Other	0.000361	0.000330

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.342
• ghis: 0.401

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: Lrrc14b

Gene ontology

• Cellular component: cytoplasm