NYAP2

protein-coding

neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2

Gene summary

Predicted to be involved in neuron projection morphogenesis and phosphatidylinositol 3-kinase/protein kinase B signal transduction. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

KIAA1486

MANE transcript

NM_001371273.1

Inheritance

—

ClinVar variants

U:89B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.42

Max pathogenic AF

—

Genomic locus

chr2:225,399,710-225,729,887

External References & Databases

Ensembl (ENSG00000144460)

Transcript & Mutation Effects

hg38 • Region Span ~330.2 kb

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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 NYAP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 92

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001371273.1. 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				2 clinvar	1 clinvar	3
missense			87 clinvar	3 clinvar		90
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	89	5	1	95

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001371273.1	RefSeq	NP_001358202.1	6	MANE Select
ENST00000272907.8	Ensembl	ENSP00000272907.7	6	MANE Select
NM_020864.2	RefSeq	NP_065915.1	5	Standard
ENST00000636099.1	Ensembl	ENSP00000490942.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

phosphatidylinositol 3-kinase signaling
neuron projection morphogenesis

Molecular Function

protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000272907
Coding exons: 5
Length: 253371
Individuals with no LoFs: 124628
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 124639
p: 0.0000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.789	360	405	0.890	0.0000263	4162
Missense (PolyPhen)		122	162.75	0.74963		1614
Synonymous	-0.0310	183	182	1.00	0.0000141	1368
Loss of Function	2.65	10	24.0	0.416	0.00000156	266

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000056	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000064	0.000044	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Activates PI3K and concomitantly recruits the WAVE1 complex to the close vicinity of PI3K and regulates neuronal morphogenesis. {ECO:0000250}.;

Intolerance Scores

RVIS EVS: -0.02
RVIS percentile EVS: 52.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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