ELFN1

protein-coding

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

Gene summary

Predicted to enable signaling receptor activity. Predicted to be involved in chemical synaptic transmission and synapse organization. Predicted to act upstream of or within several processes, including synapse assembly; synaptic signaling; and visual perception. Predicted to be located in dendrite and excitatory synapse. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

PPP1R28

MANE transcript

NM_001128636.4

Inheritance

—

ClinVar variants

P:4U:165B:44

Top phenotype

Dursun-Ozgul neurodevelopmental syndrome

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr7:1,665,745-1,747,946

External References & Databases

Ensembl (ENSG00000225968)

Transcript & Mutation Effects

hg38 • Region Span ~82.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ELFN1 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 185

not providedTotal: 34

Dursun-Ozgul neurodevelopmental syndromeTotal: 5

ELFN1-related disorderTotal: 1

Developmental and Epileptic Encephalopathy with Joint LaxityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001128636.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				29 clinvar	5 clinvar	34
missense	1 clinvar		164 clinvar	8 clinvar	2 clinvar	175
nonsense			1 clinvar			1
start loss						0
frameshift	2 clinvar	1 clinvar				3
splice donor/acceptor (+/-2bp)						0
Total	3	1	165	37	7	213

Highest pathogenic variant AF is 7.138411e-7

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 47 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001128636.4	RefSeq	NP_001122108.1	1	MANE Select
ENST00000424383.5	Ensembl	ENSP00000456548.1	1	MANE Select
NM_001394187.1	RefSeq	NP_001381116.1	1	Standard
NM_001394188.1	RefSeq	NP_001381117.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of phosphatase activity
negative regulation of phosphoprotein phosphatase activity
synapse organization

Molecular Function

protein phosphatase inhibitor activity

Cellular Component

extracellular space
integral component of membrane
dendrite
extracellular matrix
excitatory synapse

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000424383
Coding exons: 1
Length: 59836
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.44	359	515	0.698	0.0000381	5160
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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