NPIPB2

nuclear pore complex interacting protein family member B2

Basic information

Region (hg38): 16:11927258-11976643

Links

ENSG00000234719 ∙ NCBI:729978 ∙ ∙ HGNC:37451 ∙ Uniprot:A6NJ64 ∙ 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 NPIPB2 gene.

• Inborn genetic diseases (5 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPIPB2 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			7		1	8
Total	0	0	7	1	1

Variants in NPIPB2

This is a list of pathogenic ClinVar variants found in the NPIPB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-11927438-ATGG-A			Likely benign (Jul 01, 2023)
16-11965340-G-C			Uncertain significance (Mar 30, 2021)
16-11965388-A-C		not specified	Uncertain significance (Jan 23, 2024)
16-11965407-G-A		not specified	Uncertain significance (Sep 06, 2022)
16-11965427-C-A		not specified	Uncertain significance (Dec 13, 2022)
16-11966206-T-G		not specified	Uncertain significance (Mar 20, 2023)
16-11966287-T-G			Uncertain significance (Mar 30, 2021)
16-11966336-A-G		not specified	Uncertain significance (Nov 06, 2023)
16-11967672-C-T		not specified	Uncertain significance (Sep 13, 2023)
16-11967755-A-G		not specified	Uncertain significance (Nov 28, 2023)
16-11967786-G-T		not specified	Uncertain significance (Sep 23, 2023)
16-11967816-C-T		Desmoplastic small round cell tumor	other (May 01, 2016)
16-11967820-G-C			Benign (Feb 26, 2018)
16-11967839-G-T		not specified	Uncertain significance (Oct 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPIPB2	protein_coding	protein_coding	ENST00000399147	8	49271

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.97e-8	0.0943	118696	0	100	118796	0.000421

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.51	250	191	1.31	0.0000108	2497
Missense in Polyphen		91	79.412	1.1459		1208
Synonymous	-1.86	92	72.0	1.28	0.00000449	754
Loss of Function	-0.285	11	10.0	1.10	4.25e-7	174

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00350	0.00343
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000162	0.000161
Middle Eastern	0.00	0.00
South Asian	0.000196	0.000196
Other	0.000169	0.000168

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• ghis: 0.508