LRRN4CL

LRRN4 C-terminal like, the group of Fibronectin type III domain containing

Basic information

Region (hg38): 11:62686406-62689530

Links

ENSG00000177363 ∙ NCBI:221091 ∙ ∙ HGNC:33724 ∙ Uniprot:Q8ND94 ∙ 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 LRRN4CL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRN4CL 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			19	1		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	19	1	0

Variants in LRRN4CL

This is a list of pathogenic ClinVar variants found in the LRRN4CL region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62687802-C-T		not specified	Uncertain significance (Oct 27, 2022)
11-62687817-G-C		not specified	Uncertain significance (Nov 21, 2022)
11-62687823-C-A		not specified	Uncertain significance (Jan 04, 2024)
11-62687841-C-G		not specified	Uncertain significance (Nov 10, 2021)
11-62687848-G-C		not specified	Uncertain significance (Nov 07, 2022)
11-62687871-G-A		not specified	Uncertain significance (Jan 18, 2023)
11-62687884-G-C		not specified	Uncertain significance (Nov 10, 2021)
11-62687920-G-C		not specified	Uncertain significance (Jan 26, 2022)
11-62687957-G-T		not specified	Uncertain significance (Jan 04, 2024)
11-62688076-G-T		not specified	Uncertain significance (Jan 18, 2023)
11-62688090-A-C		not specified	Uncertain significance (Jan 31, 2024)
11-62688100-T-C		not specified	Uncertain significance (Jun 17, 2024)
11-62688124-G-C		not specified	Uncertain significance (May 03, 2023)
11-62688183-G-A		not specified	Uncertain significance (Mar 29, 2023)
11-62688247-T-A		not specified	Likely benign (Dec 16, 2023)
11-62688257-G-C		not specified	Uncertain significance (Oct 11, 2023)
11-62688297-C-T		not specified	Uncertain significance (May 30, 2023)
11-62688310-C-G		not specified	Uncertain significance (Sep 20, 2023)
11-62688357-T-C		not specified	Uncertain significance (May 13, 2022)
11-62688439-C-T		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRN4CL	protein_coding	protein_coding	ENST00000317449	1	3498

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000204	0.162	124187	0	35	124222	0.000141

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.108	143	147	0.975	0.00000948	1463
Missense in Polyphen		47	47.339	0.99284		485
Synonymous	1.06	59	70.3	0.840	0.00000521	529
Loss of Function	-0.925	6	4.00	1.50	1.72e-7	40

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000257	0.000249
Ashkenazi Jewish	0.00164	0.00160
East Asian	0.0000549	0.0000546
Finnish	0.00	0.00
European (Non-Finnish)	0.0000563	0.0000538
Middle Eastern	0.0000549	0.0000546
South Asian	0.000198	0.000196
Other	0.000171	0.000164

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.141
• hipred: N
• hipred_score: 0.153
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0546

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrn4cl

Gene ontology

• Cellular component: integral component of membrane