NPAP1

nuclear pore associated protein 1

Basic information

Region (hg38): 15:24675775-24683393

Previous symbols: [ "C15orf2" ]

Links

ENSG00000185823 ∙ NCBI:23742 ∙ OMIM:610922 ∙ HGNC:1190 ∙ Uniprot:Q9NZP6 ∙ 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 NPAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPAP1 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				8	4	12
missense			58	11	6	75
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	58	19	10

Variants in NPAP1

This is a list of pathogenic ClinVar variants found in the NPAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-24675889-T-C		not specified	Uncertain significance (Sep 26, 2023)
15-24675898-G-C		not specified	Uncertain significance (Sep 25, 2023)
15-24675936-C-T			Benign (Mar 30, 2018)
15-24675947-C-T		not specified	Uncertain significance (Mar 16, 2022)
15-24675955-C-T		not specified	Uncertain significance (Feb 02, 2022)
15-24675976-C-T		not specified	Uncertain significance (Jan 11, 2023)
15-24675998-C-G		not specified	Uncertain significance (Jun 02, 2023)
15-24676003-C-T			Likely benign (Sep 01, 2024)
15-24676033-C-T		not specified	Uncertain significance (Jul 16, 2024)
15-24676072-A-C		not specified	Uncertain significance (May 23, 2023)
15-24676111-C-G		not specified	Uncertain significance (May 31, 2023)
15-24676114-G-A		not specified	Uncertain significance (Sep 14, 2022)
15-24676145-C-T			Likely benign (Nov 01, 2023)
15-24676165-C-T			Benign (Apr 06, 2018)
15-24676176-G-C			Likely benign (Apr 03, 2018)
15-24676197-C-A		not specified	Uncertain significance (Aug 14, 2023)
15-24676219-C-T		not specified	Uncertain significance (May 25, 2022)
15-24676229-G-T		not specified	Uncertain significance (Jun 16, 2022)
15-24676231-A-T		not specified	Uncertain significance (Dec 08, 2023)
15-24676258-C-G		not specified	Uncertain significance (May 26, 2024)
15-24676268-C-A		not specified	Uncertain significance (May 16, 2022)
15-24676277-C-A		not specified	Uncertain significance (Jul 14, 2024)
15-24676289-T-A		not specified	Uncertain significance (Aug 28, 2023)
15-24676346-T-G			Benign (May 08, 2017)
15-24676364-C-T		not specified	Uncertain significance (May 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPAP1	protein_coding	protein_coding	ENST00000329468	1	8053

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0170	629	630	0.998	0.0000339	7352
Missense in Polyphen		98	103.28	0.94888		1263
Synonymous	-0.315	263	257	1.03	0.0000151	2600
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in spermatogenesis.
• Pathway: Prader-Willi and Angelman Syndrome (Consensus)

Recessive Scores

• pRec: 0.0581

Intolerance Scores

• rvis_EVS: 3.55
• rvis_percentile_EVS: 99.49

Haploinsufficiency Scores

• pHI: 0.0552
• hipred: N
• hipred_score: 0.316

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Gene ontology

• Biological process: protein import into nucleus;multicellular organism development;spermatogenesis;cell differentiation
• Cellular component: nuclear inner membrane;nuclear pore;nucleoplasm
• Molecular function: molecular_function;nuclear localization sequence binding;structural constituent of nuclear pore