NPAP1

protein-coding

nuclear pore associated protein 1

Gene summary

This intronless retrogene is located in the Prader-Willi syndrome region on chromosome 15. This gene exhibits tissue-specific imprinting. Expression in adult testis and brain is biallelic, while expression in fetal brain is monoallelic and only from the paternal chromosome. The encoded protein is associated with the nuclear pore complex. [provided by RefSeq, Mar 2021]

Previous symbols:

C15orf2

MANE transcript

NM_018958.3

Inheritance

—

ClinVar variants

U:160B:46

Top phenotype

Prader-Willi syndrome

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chr15:24,675,775-24,683,393

External References & Databases

Ensembl (ENSG00000185823)

Transcript & Mutation Effects

hg38 • Region Span ~7.6 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 NPAP1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 175

not providedTotal: 36

Prader-Willi syndromeTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018958.3. 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				15 clinvar	3 clinvar	18
missense			159 clinvar	24 clinvar	4 clinvar	187
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	160	39	7	206

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018958.3	RefSeq	NP_061831.2	1	MANE Select
ENST00000329468.5	Ensembl	ENSP00000333735.3	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Prader-Willi and Angelman Syndrome

Biological Process

protein import into nucleus
multicellular organism development
spermatogenesis
cell differentiation

Molecular Function

molecular_function
nuclear localization sequence binding
structural constituent of nuclear pore

Cellular Component

nuclear inner membrane
nuclear pore
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000329468
Coding exons: 1
Length: 8053

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

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

Function: FUNCTION: May be involved in spermatogenesis.;

Recessive Scores

pRec: 0.0581

Intolerance Scores

RVIS EVS: 3.55
RVIS percentile EVS: 99.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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