SYAP1

synapse associated protein 1

Basic information

Region (hg38): X:16719611-16765340

Links

ENSG00000169895 ∙ NCBI:94056 ∙ ∙ HGNC:16273 ∙ Uniprot:Q96A49 ∙ 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 SYAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYAP1 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						0
missense			10	2		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	2	0

Variants in SYAP1

This is a list of pathogenic ClinVar variants found in the SYAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-16719792-G-A		not specified	Uncertain significance (Feb 17, 2023)
X-16719801-C-T			Likely benign (Apr 01, 2023)
X-16719813-C-G		not specified	Likely benign (Feb 27, 2023)
X-16719822-C-T		not specified	Uncertain significance (Jun 07, 2024)
X-16719832-G-T		not specified	Uncertain significance (Jun 10, 2024)
X-16719845-G-A		not specified	Uncertain significance (Mar 30, 2024)
X-16719848-C-G		not specified	Uncertain significance (Oct 30, 2023)
X-16736179-A-T		not specified	Uncertain significance (May 09, 2023)
X-16743773-G-A		not specified	Uncertain significance (Oct 25, 2023)
X-16743785-A-G		not specified	Uncertain significance (Mar 21, 2024)
X-16743827-C-G		not specified	Uncertain significance (Jul 20, 2021)
X-16743830-G-A		not specified	Uncertain significance (May 15, 2024)
X-16754985-G-A		not specified	Uncertain significance (Jun 13, 2024)
X-16755051-G-A		not specified	Uncertain significance (Dec 17, 2023)
X-16755052-A-G		not specified	Uncertain significance (Dec 17, 2023)
X-16755070-G-A		not specified	Uncertain significance (Jun 05, 2023)
X-16756681-C-T		not specified	Uncertain significance (Apr 19, 2023)
X-16757256-A-C		not specified	Uncertain significance (Apr 08, 2024)
X-16757300-G-A		not specified	Uncertain significance (Jun 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYAP1	protein_coding	protein_coding	ENST00000380155	9	45705

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.943	0.0568	113639	0	1	113640	0.00000440

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	90	127	0.710	0.00000961	2327
Missense in Polyphen		25	42.811	0.58397		730
Synonymous	0.338	49	52.1	0.940	0.00000442	629
Loss of Function	3.15	1	13.5	0.0742	9.34e-7	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000796	0.0000628
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000796	0.0000628
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in adipocyte differentiation by promoting mTORC2-mediated phosphorylation of AKT1 at 'Ser-473' after growth factor stimulation (PubMed:23300339). {ECO:0000269|PubMed:23300339}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.104
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.0761
• hipred: Y
• hipred_score: 0.654
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.148

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syap1

Gene ontology

• Biological process: cell differentiation;cellular response to insulin stimulus;cellular response to platelet-derived growth factor stimulus;TORC2 signaling;positive regulation of fat cell differentiation;cellular response to epidermal growth factor stimulus;positive regulation of protein serine/threonine kinase activity;positive regulation of protein homodimerization activity;cellular response to insulin-like growth factor stimulus
• Cellular component: nucleoplasm;Golgi apparatus;cytosol;cell junction;axon;dendrite;growth cone;extrinsic component of cytoplasmic side of plasma membrane;presynaptic membrane;perikaryon;postsynaptic membrane;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: protein binding