NAPSA

napsin A aspartic peptidase, the group of Peptidase family A1

Basic information

Region (hg38): 19:50358472-50365830

Links

ENSG00000131400 ∙ NCBI:9476 ∙ OMIM:605631 ∙ HGNC:13395 ∙ Uniprot:O96009 ∙ 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 NAPSA gene.

• not_specified (59 variants)
• not_provided (2 variants)
• Myoepithelial_tumor (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAPSA gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004851.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			58	2	1	61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	2	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAPSA	protein_coding	protein_coding	ENST00000253719	9	7354

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.17e-14	0.00908	125628	0	120	125748	0.000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.158	252	259	0.972	0.0000154	2662
Missense in Polyphen		96	112.56	0.85291		1180
Synonymous	0.363	112	117	0.957	0.00000752	941
Loss of Function	-0.456	19	17.0	1.12	8.70e-7	186

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00538	0.00539
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000954	0.0000924
European (Non-Finnish)	0.000158	0.000158
Middle Eastern	0.000109	0.000109
South Asian	0.000198	0.000196
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in processing of pneumocyte surfactant precursors.
• Pathway: Lysosome - Homo sapiens (human);Surfactant metabolism;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.816
• rvis_EVS: -0.04
• rvis_percentile_EVS: 50.45

Haploinsufficiency Scores

• pHI: 0.0905
• hipred: N
• hipred_score: 0.123
• ghis: 0.392

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.121

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Napsa

Gene ontology

• Biological process: proteolysis;protein catabolic process;membrane protein proteolysis;surfactant homeostasis;cellular protein metabolic process
• Cellular component: extracellular space;lysosome;extracellular exosome;alveolar lamellar body;multivesicular body lumen
• Molecular function: endopeptidase activity;aspartic-type endopeptidase activity;peptidase activity