NPIPA5

Gene

nuclear pore complex interacting protein family member A5

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

MANE transcript

NM_001277325.2

Inheritance

—

ClinVar variants

U:2B:3

Top phenotype

Oromandibular-limb hypogenesis spectrum

gnomAD constraint

pLI —, LoF o/e 0.75

Max pathogenic AF

—

Genomic locus

chr16:15,363,628-15,381,047

External References & Databases

Ensembl (ENSG00000183793)

NCBI Gene (100288332)

Transcript & Mutation Effects

hg38 • Region Span ~17.4 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NPIPA5 variants in ClinVar

3 Conditions Cataloged

not providedTotal: 3

not specifiedTotal: 2

Oromandibular-limb hypogenesis spectrumTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001277325.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			2 clinvar	1 clinvar		3
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	2	3	0	5

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001277325.2	RefSeq	NP_001264254.1	8	MANE Select
ENST00000360151.9	Ensembl	ENSP00000433597.1	8	MANE Select
NM_001351200.1	RefSeq	NP_001338129.1	8	Standard
ENST00000534094.1	Ensembl	ENSP00000435611.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360151
Coding exons: 8
Length: 17389
Individuals with no LoFs: 104663
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 104665
p: 0.00000955

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.95	128	79.2	1.62	0.00000423	2157
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0.000069	0.000069	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR): N

Gene Damage Prediction

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