NYAP2

neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2

Basic information

Region (hg38): 2:225399710-225729887

Previous symbols: [ "KIAA1486" ]

Links

ENSG00000144460 ∙ NCBI:57624 ∙ OMIM:615478 ∙ HGNC:29291 ∙ Uniprot:Q9P242 ∙ 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 NYAP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NYAP2 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	2
missense			51	1		52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	52	2	1

Variants in NYAP2

This is a list of pathogenic ClinVar variants found in the NYAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-225408941-C-G		not specified	Uncertain significance (Jul 21, 2021)
2-225408977-G-A		not specified	Uncertain significance (Mar 04, 2025)
2-225408986-A-G		not specified	Uncertain significance (Feb 16, 2023)
2-225409058-G-A		not specified	Uncertain significance (Jun 14, 2022)
2-225409073-C-T		not specified	Uncertain significance (Oct 08, 2024)
2-225409074-G-T		not specified	Uncertain significance (Dec 06, 2023)
2-225409085-G-C		not specified	Uncertain significance (Jun 03, 2024)
2-225513375-G-A		not specified	Uncertain significance (May 14, 2024)
2-225513391-G-A		not specified	Uncertain significance (Dec 19, 2022)
2-225513399-G-A		not specified	Uncertain significance (Jul 02, 2024)
2-225513421-A-C		not specified	Uncertain significance (Oct 09, 2024)
2-225513499-G-A		not specified	Uncertain significance (Feb 23, 2023)
2-225513544-G-T		not specified	Uncertain significance (Dec 01, 2022)
2-225582004-A-G		not specified	Uncertain significance (Jan 07, 2025)
2-225582088-G-A		not specified	Uncertain significance (Nov 25, 2024)
2-225582110-G-A		not specified	Uncertain significance (Sep 15, 2021)
2-225582129-C-A		not specified	Uncertain significance (Dec 08, 2023)
2-225582240-A-G		not specified	Uncertain significance (Feb 25, 2025)
2-225582264-G-T		not specified	Likely benign (Feb 10, 2022)
2-225582303-T-C		not specified	Uncertain significance (Jun 04, 2024)
2-225582304-G-C		not specified	Uncertain significance (Jun 04, 2024)
2-225582316-C-T		not specified	Uncertain significance (Aug 12, 2024)
2-225582331-A-C		not specified	Uncertain significance (Jul 05, 2024)
2-225582342-G-A		not specified	Uncertain significance (Dec 24, 2024)
2-225582342-G-C		not specified	Uncertain significance (May 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NYAP2	protein_coding	protein_coding	ENST00000272907	5	253371

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000308	0.997	124628	0	11	124639	0.0000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.789	360	405	0.890	0.0000263	4162
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000562	0.0000556
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.0000644	0.0000442
Middle Eastern	0.0000562	0.0000556
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.654
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nyap2
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: phosphatidylinositol 3-kinase signaling;neuron projection morphogenesis
• Molecular function: protein binding