LRFN5

leucine rich repeat and fibronectin type III domain containing 5, the group of Ig-like cell adhesion molecule family|Fibronectin type III domain containing|I-set domain containing

Basic information

Region (hg38): 14:41606876-41904549

Previous symbols: [ "C14orf146" ]

Links

ENSG00000165379 ∙ NCBI:145581 ∙ OMIM:612811 ∙ HGNC:20360 ∙ Uniprot:Q96NI6 ∙ 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 LRFN5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRFN5 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				5	5	10
missense			21		1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	21	5	6

Variants in LRFN5

This is a list of pathogenic ClinVar variants found in the LRFN5 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-41886641-T-C		not specified	Uncertain significance (Aug 12, 2021)
14-41886769-C-A		not specified	Uncertain significance (Jan 24, 2023)
14-41886802-A-C		LRFN5-related disorder	Benign (May 20, 2019)
14-41886883-A-G		LRFN5-related disorder	Likely benign (Dec 31, 2019)
14-41886977-A-G		not specified	Uncertain significance (Nov 21, 2023)
14-41887041-C-G		not specified	Uncertain significance (Jan 03, 2022)
14-41887066-C-T		LRFN5-related disorder	Benign (Mar 11, 2019)
14-41887092-A-G		not specified	Uncertain significance (Mar 06, 2023)
14-41887200-C-T		Inborn genetic diseases	Uncertain significance (Jan 13, 2014)
14-41887219-T-C		LRFN5-related disorder	Likely benign (Nov 15, 2018)
14-41887413-G-A		not specified	Uncertain significance (May 27, 2022)
14-41887440-G-A		not specified	Uncertain significance (Feb 21, 2024)
14-41887446-T-A		not specified	Uncertain significance (Apr 08, 2024)
14-41887494-C-T		Inborn genetic diseases	Uncertain significance (Jan 13, 2014)
14-41887570-G-A		LRFN5-related disorder	Likely benign (Mar 25, 2019)
14-41887599-G-A		not specified	Uncertain significance (May 28, 2024)
14-41887619-A-T		not specified	Uncertain significance (Aug 28, 2023)
14-41887727-C-G		not specified	Uncertain significance (Jan 23, 2024)
14-41887846-A-G		LRFN5-related disorder	Likely benign (Apr 05, 2019)
14-41887895-G-A		not specified	Uncertain significance (Apr 06, 2024)
14-41887914-C-T		not specified	Uncertain significance (Dec 26, 2023)
14-41887952-G-A		not specified	Uncertain significance (Aug 16, 2022)
14-41888009-A-G		not specified	Uncertain significance (Sep 12, 2023)
14-41891339-A-G		not specified	Uncertain significance (Jul 26, 2022)
14-41891422-A-T		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRFN5	protein_coding	protein_coding	ENST00000298119	4	296980

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.559	0.441	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.78	288	386	0.746	0.0000200	4735
Missense in Polyphen		68	141.4	0.48091		1806
Synonymous	-0.439	151	144	1.05	0.00000748	1458
Loss of Function	3.29	4	19.8	0.202	0.00000102	267

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000125
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell adhesion molecule that mediates homophilic cell- cell adhesion in a Ca(2+)-independent manner. Promotes neurite outgrowth in hippocampal neurons. {ECO:0000269|PubMed:18227064, ECO:0000269|PubMed:18585462}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.180
• rvis_EVS: -0.87
• rvis_percentile_EVS: 10.65

Haploinsufficiency Scores

• pHI: 0.444
• hipred: Y
• hipred_score: 0.800
• ghis: 0.632

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.134

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrfn5

Gene ontology

• Biological process: synaptic membrane adhesion;regulation of presynapse assembly
• Cellular component: cell surface;glutamatergic synapse;GABA-ergic synapse;integral component of postsynaptic density membrane