NAPSA

napsin A aspartic peptidase, the group of Peptidase family A1

Basic information

Region (hg38): 19:50358471-50365830

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.

• Inborn genetic diseases (23 variants)
• not provided (2 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.

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					1	1
missense			23		1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	2

Variants in NAPSA

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

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

Position	Type	Phenotype	Significance	ClinVar
19-50358590-C-A		not specified	Uncertain significance (Aug 21, 2023)
19-50358594-G-C			Benign (Jan 19, 2018)
19-50358606-G-C		not specified	Uncertain significance (Dec 16, 2022)
19-50358747-C-A		not specified	Uncertain significance (Dec 12, 2023)
19-50359054-C-G		not specified	Uncertain significance (Jun 27, 2022)
19-50359058-G-A		not specified	Uncertain significance (Nov 21, 2022)
19-50359508-C-T		not specified	Uncertain significance (Oct 05, 2021)
19-50359531-A-G		not specified	Uncertain significance (Apr 07, 2022)
19-50359576-A-G		not specified	Uncertain significance (Aug 10, 2021)
19-50359609-C-T		not specified	Uncertain significance (Apr 22, 2022)
19-50359631-C-T		not specified	Uncertain significance (Feb 10, 2022)
19-50359744-C-T		not specified	Uncertain significance (Aug 11, 2022)
19-50359764-G-A		not specified	Uncertain significance (Mar 02, 2023)
19-50359783-C-T		not specified	Uncertain significance (Aug 10, 2021)
19-50359803-T-C		not specified	Uncertain significance (Apr 22, 2022)
19-50359817-C-T			Benign (Jan 19, 2018)
19-50359840-C-G		not specified	Uncertain significance (May 26, 2022)
19-50361000-C-A		Myoepithelial tumor	Uncertain significance (Nov 01, 2022)
19-50361058-T-C		not specified	Uncertain significance (Feb 07, 2023)
19-50361063-A-T		not specified	Uncertain significance (Feb 07, 2023)
19-50361101-C-A		not specified	Uncertain significance (Dec 08, 2023)
19-50361677-C-T		not specified	Uncertain significance (Jul 06, 2021)
19-50361698-G-A		not specified	Uncertain significance (May 04, 2022)
19-50361712-T-A		not specified	Uncertain significance (Feb 16, 2023)
19-50361718-G-A		not specified	Uncertain significance (Aug 20, 2023)

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