NPIPB3

nuclear pore complex interacting protein family member B3

Basic information

Region (hg38): 16:21402237-21448567

Previous symbols: [ "NPIPL3" ]

Links

ENSG00000169246 ∙ NCBI:23117 ∙ OMIM:619984 ∙ HGNC:28989 ∙ Uniprot:Q92617 ∙ 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 NPIPB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPIPB3 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						0
missense			1	1		2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	1	0

Variants in NPIPB3

This is a list of pathogenic ClinVar variants found in the NPIPB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-21402618-G-A		not specified	Uncertain significance (Oct 05, 2021)
16-21402885-G-A		not specified	Uncertain significance (Aug 13, 2021)
16-21404765-G-A		not specified	Uncertain significance (Aug 10, 2021)
16-21404768-C-T		not specified	Uncertain significance (Jan 22, 2025)
16-21404851-G-A		not specified	Uncertain significance (Sep 01, 2021)
16-21405020-C-G		not specified	Uncertain significance (Aug 13, 2021)
16-21405198-C-G		not specified	Uncertain significance (Jul 13, 2021)
16-21405223-G-A		not specified	Uncertain significance (Aug 09, 2021)
16-21410938-T-C		not specified	Likely benign (Aug 16, 2021)
16-21424993-C-T		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPIPB3	protein_coding	protein_coding	ENST00000458643	10	46331

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00233	0.335	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.683	69	54.8	1.26	0.00000349	6159
Missense in Polyphen		51	38.478	1.3254		3200
Synonymous	-2.70	39	22.6	1.72	0.00000152	2170
Loss of Function	-1.14	3	1.50	2.01	6.42e-8	231

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

• hipred: N
• hipred_score: 0.187
• ghis: 0.609

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;nucleoplasm;integral component of membrane
• Molecular function: molecular_function