NPIPA1

nuclear pore complex interacting protein family member A1

Basic information

Region (hg38): 16:14922801-14952060

Previous symbols: [ "NPIP" ]

Links

ENSG00000183426 ∙ NCBI:9284 ∙ OMIM:606406 ∙ HGNC:7909 ∙ Uniprot:Q9UND3 ∙ 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 NPIPA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPIPA1 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	2		25
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	3	0

Variants in NPIPA1

This is a list of pathogenic ClinVar variants found in the NPIPA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-14945599-C-T		not specified	Uncertain significance (Aug 17, 2021)
16-14945659-G-A		not specified	Uncertain significance (Jun 24, 2022)
16-14945662-G-A		not specified	Uncertain significance (Dec 19, 2022)
16-14945846-T-C		not specified	Uncertain significance (Mar 29, 2022)
16-14945871-A-C		not specified	Uncertain significance (Aug 12, 2021)
16-14945938-C-T		not specified	Uncertain significance (Oct 31, 2023)
16-14945944-G-A		not specified	Uncertain significance (Apr 25, 2023)
16-14951631-T-C		not specified	Uncertain significance (May 20, 2024)
16-14951640-G-A		not specified	Likely benign (Jul 06, 2021)
16-14951652-G-C		not specified	Uncertain significance (Dec 15, 2022)
16-14951691-A-T		not specified	Uncertain significance (Jul 19, 2023)
16-14951742-T-C		not specified	Uncertain significance (Mar 18, 2024)
16-14951768-C-A		not specified	Uncertain significance (Nov 01, 2022)
16-14951774-G-A		not specified	Uncertain significance (Jul 06, 2021)
16-14951777-T-C			Likely benign (Jul 01, 2022)
16-14951780-C-G		not specified	Uncertain significance (Aug 02, 2021)
16-14951781-T-A		not specified	Uncertain significance (Aug 02, 2023)
16-14951786-A-T		not specified	Conflicting classifications of pathogenicity (Dec 08, 2023)
16-14951787-C-A		not specified	Conflicting classifications of pathogenicity (Nov 28, 2023)
16-14951792-C-G		not specified	Uncertain significance (Dec 27, 2022)
16-14951798-C-T		not specified	Uncertain significance (Jul 06, 2021)
16-14951811-C-T		not specified	Uncertain significance (Mar 29, 2023)
16-14951821-T-G		not specified	Uncertain significance (Aug 23, 2021)
16-14951841-C-T		not specified	Uncertain significance (Jul 15, 2021)
16-14951842-G-A		not specified	Likely benign (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPIPA1	protein_coding	protein_coding	ENST00000328085	8	29257

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.322	0.499	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.657	75	60.6	1.24	0.00000309	2167
Missense in Polyphen		22	20.801	1.0576		950
Synonymous	-0.823	30	24.8	1.21	0.00000142	652
Loss of Function	0.573	0	0.383	0.00	1.61e-8	166

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.384
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: 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 transport;mRNA transport
• Cellular component: nuclear pore;nucleoplasm;nuclear membrane