NPIPB11

protein-coding

nuclear pore complex interacting protein family member B11

Gene summary

Predicted to act upstream of or within prevention of polyspermy. Predicted to be located in external side of plasma membrane and sperm head plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001310137.5

Inheritance

—

ClinVar variants

B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.49

Max pathogenic AF

—

Genomic locus

chr16:29,381,310-29,406,711

External References & Databases

Ensembl (ENSG00000254206)

Transcript & Mutation Effects

hg38 • Region Span ~25.4 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 NPIPB11 variants in ClinVar

2 Conditions Cataloged

not providedTotal: 5

not specifiedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001310137.5. 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				3 clinvar		3
missense				2 clinvar		2
nonsense						0
start loss						0
frameshift				2 clinvar		2
splice donor/acceptor (+/-2bp)						0
Total	0	0	0	7	0	7

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001310137.5	RefSeq	NP_001297066.2	7	MANE Select
ENST00000698511.1	Ensembl	ENSP00000513761.1	7	MANE Select
ENST00000524087.5	Ensembl	ENSP00000430853.1	7	Standard
ENST00000524087.6	Ensembl	ENSP00000430853.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

nucleoplasm
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000524087
Coding exons: 7
Length: 22676
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	-2.15	505	386	1.31	0.0000250	7215
Missense (PolyPhen)		156	141.19	1.1049		2591
Synonymous	-1.41	174	152	1.15	0.0000102	2477
Loss of Function	1.33	4	8.10	0.494	4.16e-7	145

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

Gene Damage Prediction

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