ELFN2

protein-coding

extracellular leucine rich repeat and fibronectin type III domain containing 2, 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. Predicted to act upstream of or within establishment of protein localization and gene expression. Located in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

LRRC62
PPP1R29

MANE transcript

NM_052906.5

Inheritance

—

ClinVar variants

U:122B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr22:37,367,960-37,427,479

External References & Databases

Ensembl (ENSG00000166897)

Transcript & Mutation Effects

hg38 • Region Span ~59.5 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 ELFN2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 122

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052906.5. 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				1 clinvar		1
missense			122 clinvar	2 clinvar	2 clinvar	126
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	122	3	2	127

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052906.5	RefSeq	NP_443138.2	1	MANE Select
ENST00000402918.7	Ensembl	ENSP00000385277.1	1	MANE Select
ENST00000939364.1	Ensembl	ENSP00000609423.1	1	Standard
ENST00000939364.2	Ensembl	ENSP00000609423.1	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

Molecular Function

protein phosphatase inhibitor activity

Cellular Component

extracellular space
integral component of membrane
extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000402918
Coding exons: 1
Length: 59506
Individuals with no LoFs: 125706
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125713
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.16	426	571	0.746	0.0000424	5295
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0.000098	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): 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