NPIPB7

nuclear pore complex interacting protein family member B7

Basic information

Region (hg38): 16:28456329-28472336

Previous symbols: [ "NPIPL1" ]

Links

ENSG00000233232 ∙ NCBI:440350 ∙ ∙ HGNC:33832 ∙ Uniprot:O75200 ∙ 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 NPIPB7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPIPB7 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				3		3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	4	0

Variants in NPIPB7

This is a list of pathogenic ClinVar variants found in the NPIPB7 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-28456739-C-T			Likely benign (Jun 01, 2024)
16-28456762-G-C			Likely benign (Dec 01, 2023)
16-28456861-G-C			Likely benign (Jan 01, 2023)
16-28456905-G-C			Likely benign (May 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPIPB7	protein_coding	protein_coding	ENST00000452313	7	14176

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0164	0.487	108155	0	12	108167	0.0000555

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.349	52	45.4	1.15	0.00000248	2609
Missense in Polyphen		22	18.732	1.1745		1095
Synonymous	0.268	16	17.4	0.918	9.41e-7	821
Loss of Function	-0.572	2	1.30	1.54	5.52e-8	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000279	0.000279
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000104	0.0000104
Middle Eastern	0.00	0.00
South Asian	0.0000764	0.0000764
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187
• ghis: 0.402

Gene Damage Prediction

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

Gene ontology

• Cellular component: extracellular region;nucleoplasm