NPIPA1

protein-coding

nuclear pore complex interacting protein family member A1

Gene summary

Predicted to be involved in mRNA transport and protein transport. Predicted to be located in nuclear membrane. Predicted to be part of nuclear pore. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

NPIP

MANE transcript

NM_006985.4

Inheritance

—

ClinVar variants

U:43B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr16:14,922,802-14,952,060

External References & Databases

Ensembl (ENSG00000183426)

Transcript & Mutation Effects

hg38 • Region Span ~29.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NPIPA1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 49

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006985.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			43 clinvar	5 clinvar		48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	43	6	0	49

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006985.4	RefSeq	NP_008916.2	8	MANE Select
ENST00000328085.10	Ensembl	ENSP00000331843.6	8	MANE Select
ENST00000424549.7	Ensembl	ENSP00000410814.3	6	Standard
ENST00000537062.1	Ensembl	ENSP00000445593.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein transport
mRNA transport

Cellular Component

nuclear pore
nucleoplasm
nuclear membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000328085
Coding exons: 8
Length: 29257
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.657	75	60.6	1.24	0.00000309	2167
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR): N
Essential (gene trap): N

Gene Damage Prediction

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