ELFN2

extracellular leucine rich repeat and fibronectin type III domain containing 2, the group of Fibronectin type III domain containing|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 22:37367959-37427479

Previous symbols: [ "LRRC62", "PPP1R29" ]

Links

ENSG00000166897 ∙ NCBI:114794 ∙ OMIM:620223 ∙ HGNC:29396 ∙ Uniprot:Q5R3F8 ∙ 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 ELFN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELFN2 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			38	1	2	41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	1	2

Variants in ELFN2

This is a list of pathogenic ClinVar variants found in the ELFN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-37373193-C-T		not specified	Uncertain significance (May 27, 2022)
22-37373238-G-A		not specified	Uncertain significance (Apr 07, 2022)
22-37373245-C-G		not specified	Uncertain significance (Oct 25, 2023)
22-37373301-T-C		not specified	Uncertain significance (Jul 27, 2022)
22-37373317-C-T		not specified	Uncertain significance (Dec 16, 2023)
22-37373329-G-A		not specified	Uncertain significance (Dec 05, 2022)
22-37373355-C-T		not specified	Uncertain significance (Feb 23, 2023)
22-37373395-C-T		not specified	Uncertain significance (Dec 14, 2023)
22-37373412-T-C		not specified	Uncertain significance (Oct 27, 2022)
22-37373464-C-T		not specified	Uncertain significance (May 30, 2024)
22-37373527-G-C		not specified	Uncertain significance (Apr 23, 2024)
22-37373590-C-G		not specified	Uncertain significance (May 31, 2023)
22-37373659-G-A			Likely benign (Apr 04, 2024)
22-37373688-C-T		not specified	Uncertain significance (Mar 07, 2023)
22-37373731-G-C		not specified	Uncertain significance (Sep 29, 2022)
22-37373907-T-C		not specified	Uncertain significance (May 13, 2024)
22-37373956-C-A		not specified	Uncertain significance (Oct 07, 2022)
22-37373956-C-T		not specified	Uncertain significance (Aug 12, 2021)
22-37373970-G-A		not specified	Uncertain significance (Apr 07, 2023)
22-37373988-C-G		not specified	Uncertain significance (Oct 02, 2023)
22-37373998-C-T		not specified	Uncertain significance (Jun 18, 2021)
22-37374004-C-T		not specified	Uncertain significance (Aug 10, 2021)
22-37374007-C-T		not specified	Uncertain significance (Nov 05, 2021)
22-37374115-G-A		not specified	Uncertain significance (Jun 18, 2021)
22-37374135-A-G		not specified	Uncertain significance (Jun 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELFN2	protein_coding	protein_coding	ENST00000402918	1	59506

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.965	0.0352	125706	0	7	125713	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.16	426	571	0.746	0.0000424	5295
Missense in Polyphen		117	212.66	0.55017		2020
Synonymous	-0.276	292	286	1.02	0.0000246	1762
Loss of Function	3.64	2	19.2	0.104	9.13e-7	225

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000981	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits phosphatase activity of protein phosphatase 1 (PP1) complexes. {ECO:0000269|PubMed:19389623}.

Intolerance Scores

• loftool: 0.00820
• rvis_EVS: -1.84
• rvis_percentile_EVS: 2.08

Haploinsufficiency Scores

• pHI: 0.182
• hipred: Y
• hipred_score: 0.728
• ghis: 0.614

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: Elfn2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of phosphatase activity;negative regulation of phosphoprotein phosphatase activity
• Cellular component: extracellular space;integral component of membrane;extracellular matrix
• Molecular function: protein phosphatase inhibitor activity