LRRC14

leucine rich repeat containing 14

Basic information

Region (hg38): 8:144517992-144525172

Links

ENSG00000160959 ∙ NCBI:9684 ∙ OMIM:619368 ∙ HGNC:20419 ∙ Uniprot:Q15048 ∙ 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 LRRC14 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC14 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			26	3		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			31	5		36
Total	0	0	57	8	1

Variants in LRRC14

This is a list of pathogenic ClinVar variants found in the LRRC14 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-144518144-C-T			Likely benign (Apr 24, 2019)
8-144519750-A-G		not specified	Uncertain significance (Apr 29, 2024)
8-144519798-T-C		not specified	Benign (Mar 29, 2016)
8-144519867-C-T		not specified	Uncertain significance (Jan 10, 2023)
8-144519883-C-G		not specified	Uncertain significance (Apr 25, 2022)
8-144519942-C-T		not specified	Uncertain significance (Aug 13, 2021)
8-144519960-C-T		not specified	Uncertain significance (Aug 17, 2022)
8-144519982-A-G		not specified	Uncertain significance (Dec 19, 2023)
8-144520252-G-T		not specified	Uncertain significance (Feb 16, 2023)
8-144520302-G-A		not specified	Uncertain significance (Feb 23, 2023)
8-144520326-A-T		not specified	Uncertain significance (Jul 06, 2021)
8-144520342-G-A		not specified	Uncertain significance (Feb 05, 2024)
8-144520365-G-T		not specified	Uncertain significance (Oct 17, 2023)
8-144520374-G-A		not specified	Likely benign (Apr 26, 2023)
8-144520390-C-T		not specified	Uncertain significance (Jun 04, 2024)
8-144520418-C-A		not specified	Uncertain significance (Jul 09, 2021)
8-144520483-C-T		not specified	Uncertain significance (Jan 26, 2022)
8-144520491-C-G		not specified	Uncertain significance (Apr 22, 2024)
8-144520530-C-T		not specified	Uncertain significance (Aug 12, 2021)
8-144520575-C-T		not specified	Uncertain significance (Dec 27, 2023)
8-144520576-G-A		not specified	Uncertain significance (Jun 24, 2022)
8-144520716-G-A		not specified	Uncertain significance (Nov 21, 2022)
8-144520748-G-A		not specified	Uncertain significance (Nov 02, 2023)
8-144520752-C-G		not specified	Uncertain significance (Feb 14, 2023)
8-144520768-G-A		not specified	Uncertain significance (May 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC14	protein_coding	protein_coding	ENST00000292524	3	7182

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000173	0.896	125636	0	22	125658	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	258	316	0.816	0.0000217	3134
Missense in Polyphen		50	83.088	0.60177		920
Synonymous	-2.44	176	139	1.26	0.00000855	1127
Loss of Function	1.48	8	14.0	0.573	7.74e-7	142

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000445	0.0000440
Middle Eastern	0.000164	0.000163
South Asian	0.000131	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates Toll-like receptor-mediated NF- kappa-B signaling by disrupting IKK core complex formation through interaction with IKBKB. {ECO:0000269|PubMed:27426725}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.594
• rvis_EVS: -1
• rvis_percentile_EVS: 8.32

Haploinsufficiency Scores

• pHI: 0.0839
• hipred: Y
• hipred_score: 0.719
• ghis: 0.622

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.949

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc14

Gene ontology

• Biological process: negative regulation of NF-kappaB transcription factor activity;negative regulation of toll-like receptor signaling pathway
• Cellular component: cytoplasm
• Molecular function: kinase binding