NYAP1

neuronal tyrosine phosphorylated phosphoinositide-3-kinase adaptor 1

Basic information

Region (hg38): 7:100483927-100494802

Previous symbols: [ "C7orf51", "KIAA1486L" ]

Links

ENSG00000166924 ∙ NCBI:222950 ∙ OMIM:615477 ∙ HGNC:22009 ∙ Uniprot:Q6ZVC0 ∙ 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 NYAP1 gene.

• not_specified (142 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NYAP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000173564.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	1	4
missense			133	7		140
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	133	10	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NYAP1	protein_coding	protein_coding	ENST00000300179	6	10873

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000830	125652	0	9	125661	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.768	450	498	0.903	0.0000309	5189
Missense in Polyphen		143	196.78	0.7267		2131
Synonymous	-0.532	232	222	1.05	0.0000146	1896
Loss of Function	4.44	1	24.9	0.0401	0.00000164	264

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000692	0.0000692
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.0000475	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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: -1.24
• rvis_percentile_EVS: 5.46

Haploinsufficiency Scores

• pHI: 0.403
• hipred: Y
• hipred_score: 0.537
• ghis: 0.587

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: Nyap1
• 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