NPIPA5

nuclear pore complex interacting protein family member A5

Basic information

Region (hg38): 16:15363628-15381047

Links

ENSG00000183793 ∙ NCBI:100288332 ∙ ∙ HGNC:41980 ∙ Uniprot:E9PKD4 ∙ 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 NPIPA5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPIPA5 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						0
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	1	0

Variants in NPIPA5

This is a list of pathogenic ClinVar variants found in the NPIPA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-15363750-G-A		Oromandibular-limb hypogenesis spectrum	Uncertain significance (-)
16-15370093-C-T			Likely benign (Feb 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPIPA5	protein_coding	protein_coding	ENST00000360151	8	17389

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.108	0.610	104663	0	2	104665	0.00000955

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.95	128	79.2	1.62	0.00000423	2157
Missense in Polyphen		54	38.725	1.3944		1102
Synonymous	-1.92	47	33.0	1.42	0.00000206	660
Loss of Function	0.268	1	1.33	0.750	5.61e-8	167

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	0.0000687	0.0000687
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N

Gene Damage Prediction

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

Gene ontology

• Cellular component: nucleoplasm