PAPLN

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

Basic information

Region (hg38): 14:73237496-73274640

Links

ENSG00000100767 ∙ NCBI:89932 ∙ OMIM:617785 ∙ HGNC:19262 ∙ Uniprot:O95428 ∙ 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 PAPLN gene.

• Inborn genetic diseases (68 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAPLN 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				2		2
missense			60	8	2	70
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	60	10	2

Variants in PAPLN

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

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

Position	Type	Phenotype	Significance	ClinVar
14-73239789-T-C		not specified	Uncertain significance (Oct 02, 2023)
14-73244741-G-A		not specified	Uncertain significance (Aug 08, 2022)
14-73245653-G-A		not specified	Uncertain significance (Jul 25, 2023)
14-73246085-G-A		not specified	Uncertain significance (Mar 02, 2023)
14-73246088-G-T		not specified	Uncertain significance (Nov 17, 2022)
14-73246092-G-A		not specified	Uncertain significance (May 03, 2023)
14-73246140-A-T		not specified	Uncertain significance (Mar 01, 2024)
14-73246146-G-A		not specified	Uncertain significance (Feb 05, 2024)
14-73246148-C-T		not specified	Uncertain significance (Sep 06, 2022)
14-73250077-C-T		not specified	Uncertain significance (Mar 24, 2023)
14-73250084-G-C		not specified	Uncertain significance (Sep 29, 2023)
14-73250938-C-T		not specified	Uncertain significance (Feb 08, 2023)
14-73251013-C-T		not specified	Uncertain significance (Nov 05, 2021)
14-73251028-G-A		not specified	Uncertain significance (May 05, 2023)
14-73251679-G-A		not specified	Uncertain significance (Jul 14, 2021)
14-73251718-C-T		not specified	Uncertain significance (Sep 25, 2023)
14-73251724-G-C		not specified	Uncertain significance (Oct 06, 2021)
14-73251762-C-T		not specified	Uncertain significance (Dec 19, 2023)
14-73251763-G-A		not specified	Uncertain significance (Mar 29, 2023)
14-73251793-G-A		not specified	Uncertain significance (Jan 23, 2024)
14-73251805-G-A		not specified	Uncertain significance (Dec 28, 2023)
14-73251818-G-A			Likely benign (Mar 01, 2022)
14-73252138-G-A		not specified	Uncertain significance (Jul 29, 2023)
14-73252660-C-G		not specified	Uncertain significance (Jan 04, 2024)
14-73252714-C-T		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAPLN	protein_coding	protein_coding	ENST00000340738	25	37144

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.49e-38	0.0000319	124292	6	1450	125748	0.00581

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.426	719	752	0.956	0.0000473	7948
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00515	0.00512
Ashkenazi Jewish	0.0158	0.0155
East Asian	0.00458	0.00447
Finnish	0.00751	0.00723
European (Non-Finnish)	0.00724	0.00676
Middle Eastern	0.00458	0.00447
South Asian	0.00495	0.00478
Other	0.00399	0.00375

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.970
• rvis_EVS: 1.27
• rvis_percentile_EVS: 93.61

Haploinsufficiency Scores

• pHI: 0.461
• hipred: N
• hipred_score: 0.207
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.183

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Papln
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: proteolysis;negative regulation of endopeptidase activity
• Cellular component: extracellular region
• Molecular function: serine-type endopeptidase inhibitor activity;peptidase activity