NPIPB5

nuclear pore complex interacting protein family member B5

Basic information

Region (hg38): 16:22479121-22536540

Links

ENSG00000243716 ∙ NCBI:100132247 ∙ ∙ HGNC:37233 ∙ Uniprot:A8MRT5 ∙ 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 NPIPB5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPIPB5 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			56	8		64
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	9	0

Variants in NPIPB5

This is a list of pathogenic ClinVar variants found in the NPIPB5 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-22527841-G-T		not specified	Likely benign (May 11, 2022)
16-22527961-C-G		not specified	Likely benign (Oct 10, 2023)
16-22533729-C-T		not specified	Uncertain significance (Apr 28, 2023)
16-22533744-A-C		not specified	Uncertain significance (Sep 16, 2021)
16-22533747-C-G		not specified	Uncertain significance (Nov 12, 2021)
16-22533798-C-G		not specified	Uncertain significance (Oct 20, 2024)
16-22533837-C-T		not specified	Uncertain significance (Jan 12, 2024)
16-22533848-G-C		not specified	Likely benign (Jul 13, 2021)
16-22533855-C-T		not specified	Uncertain significance (Aug 11, 2024)
16-22533858-C-A		not specified	Uncertain significance (Nov 08, 2024)
16-22533873-C-T		not specified	Uncertain significance (Oct 25, 2023)
16-22533944-A-G		not specified	Uncertain significance (Jul 16, 2024)
16-22533974-C-G		not specified	Uncertain significance (Nov 12, 2024)
16-22533987-C-T		not specified	Uncertain significance (Jul 09, 2021)
16-22533990-A-G		not specified	Uncertain significance (Dec 03, 2024)
16-22534010-C-T		not specified	Uncertain significance (Oct 21, 2024)
16-22534019-C-G		not specified	Uncertain significance (May 24, 2023)
16-22534038-C-G		not specified	Uncertain significance (Aug 10, 2021)
16-22534043-G-A		not specified	Uncertain significance (Nov 22, 2023)
16-22534050-C-A		not specified	Uncertain significance (May 27, 2022)
16-22534076-A-G		not specified	Uncertain significance (Aug 15, 2023)
16-22534089-G-C		not specified	Uncertain significance (Jul 14, 2023)
16-22534092-C-T		not specified	Uncertain significance (Feb 23, 2023)
16-22534094-G-A		not specified	Uncertain significance (Dec 13, 2023)
16-22534103-C-T		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPIPB5	protein_coding	protein_coding	ENST00000424340	7	57401

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.149	128	133	0.964	0.00000758	7007
Missense in Polyphen		64	69.614	0.91935		2986
Synonymous	1.24	43	54.7	0.787	0.00000338	2390
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• ghis: 0.515

Essentials

• essential_gene_CRISPR: E

Gene Damage Prediction

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

Gene ontology

• Cellular component: nucleoplasm;integral component of membrane