ELFN1

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

Basic information

Region (hg38): 7:1665745-1747946

Previous symbols: [ "PPP1R28" ]

Links

ENSG00000225968 ∙ NCBI:392617 ∙ OMIM:614964 ∙ HGNC:33154 ∙ Uniprot:P0C7U0 ∙ 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 ELFN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELFN1 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				11	11	22
missense			91	5	2	98
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	91	17	13

Variants in ELFN1

This is a list of pathogenic ClinVar variants found in the ELFN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-1744596-G-A			Likely benign (Mar 01, 2023)
7-1744603-G-A		not specified	Uncertain significance (Aug 01, 2022)
7-1744633-G-A		not specified	Uncertain significance (Aug 28, 2023)
7-1744637-CGGCCGCCA-C		Developmental and Epileptic Encephalopathy with Joint Laxity	Conflicting classifications of pathogenicity (Nov 04, 2021)
7-1744638-G-A			Benign (Dec 31, 2019)
7-1744656-C-T			Benign (Dec 31, 2019)
7-1744663-G-A		not specified	Uncertain significance (Jan 23, 2023)
7-1744670-C-T		not specified	Uncertain significance (Feb 25, 2025)
7-1744672-C-T		ELFN1-related disorder	Likely benign (Dec 31, 2019)
7-1744673-G-T		not specified	Uncertain significance (Dec 27, 2023)
7-1744800-C-G			Uncertain significance (Feb 17, 2022)
7-1744832-C-T		not specified	Uncertain significance (Jan 26, 2023)
7-1744874-A-G		not specified	Uncertain significance (Sep 29, 2023)
7-1744893-C-T			Benign (Dec 31, 2019)
7-1744899-C-T			Likely benign (May 21, 2018)
7-1744900-G-A		not specified	Uncertain significance (Feb 06, 2023)
7-1744911-G-A			Benign (Dec 31, 2019)
7-1744919-T-C		not specified	Uncertain significance (Oct 24, 2023)
7-1744922-A-T		not specified	Uncertain significance (Nov 25, 2024)
7-1744928-A-G		not specified	Uncertain significance (Mar 06, 2023)
7-1744952-G-A		not specified	Uncertain significance (May 24, 2024)
7-1744958-G-A		not specified	Uncertain significance (Jul 05, 2024)
7-1745070-C-A			Likely benign (Jun 29, 2018)
7-1745128-G-A		not specified	Uncertain significance (Jul 13, 2021)
7-1745162-G-A		not specified	Uncertain significance (Jul 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELFN1	protein_coding	protein_coding	ENST00000424383	1	59836

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00118	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.44	359	515	0.698	0.0000381	5160
Missense in Polyphen		84	156.55	0.53657		1700
Synonymous	-0.0923	264	262	1.01	0.0000223	1765
Loss of Function	4.10	0	19.6	0.00	9.06e-7	229

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Postsynaptic protein that regulates circuit dynamics in the central nervous system by modulating the temporal dynamics of interneuron recruitment. Specifically present in excitatory synapses onto oriens-lacunosum molecular (OLM) interneurons and acts as a regulator of presynaptic release probability to direct the formation of highly facilitating pyramidal-OLM synapses (By similarity). Inhibits phosphatase activity of protein phosphatase 1 (PP1) complexes. {ECO:0000250, ECO:0000269|PubMed:19389623}.

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.310

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: 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: Elfn1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

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