PAPLN

protein-coding

papilin, proteoglycan like sulfated glycoprotein, the group of ADAMTS like|I-set domain containing

Gene summary

Predicted to enable serine-type endopeptidase inhibitor activity. Predicted to be involved in extracellular matrix organization and nervous system development. Predicted to be located in basement membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001365906.3

Inheritance

—

ClinVar variants

U:243B:30

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.92

Max pathogenic AF

—

Genomic locus

chr14:73,237,497-73,274,640

External References & Databases

Ensembl (ENSG00000100767)

Transcript & Mutation Effects

hg38 • Region Span ~37.1 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 PAPLN variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 257

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001365906.3. 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			2 clinvar	3 clinvar		5
missense			233 clinvar	25 clinvar	1 clinvar	259
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar	1 clinvar		8
Total	0	0	243	29	1	273

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 50 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001365906.3	RefSeq	NP_001352835.1	26	MANE Select
ENST00000644200.2	Ensembl	ENSP00000495882.2	26	MANE Select
NM_001365907.2	RefSeq	NP_001352836.1	26	Standard
NM_173462.4	RefSeq	NP_775733.3	25	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

proteolysis
negative regulation of endopeptidase activity

Molecular Function

serine-type endopeptidase inhibitor activity
peptidase activity

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000340738
Coding exons: 25
Length: 37144
Individuals with no LoFs: 124292
Homozygous LoFs: 6
Heterozygous LoFs: 1450
Defined: 125748
p: 0.00581

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.426	719	752	0.956	0.0000473	7948
Missense (PolyPhen)		233	266.26	0.87507		2952
Synonymous	-0.370	330	322	1.03	0.0000217	2533
Loss of Function	0.599	60	65.2	0.920	0.00000341	691

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0025	0.0025	notable
Latino/Admixed American	0.0027	0.0025	notable
Ashkenazi Jewish	0.016	0.015	notable
East Asian	0.0046	0.0045	notable
Finnish	0.0075	0.0072	notable
European (Non-Finnish)	0.0072	0.0068	notable
South Asian	0.0049	0.0048	notable
Other	0.0040	0.0038	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.970
RVIS EVS: 1.27
RVIS percentile EVS: 93.61

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.183

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High