SYAP1

protein-coding

synapse associated protein 1

Gene summary

Involved in several processes, including TORC2 signaling; cellular response to epidermal growth factor stimulus; and cellular response to peptide hormone stimulus. Located in several cellular components, including Golgi apparatus; cytoplasmic side of plasma membrane; and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_032796.4

Inheritance

—

ClinVar variants

U:104B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chrX:16,719,612-16,765,340

External References & Databases

Ensembl (ENSG00000169895)

Transcript & Mutation Effects

hg38 • Region Span ~45.7 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 SYAP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 33

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032796.4. 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			10 clinvar	1 clinvar		11
missense			61 clinvar	3 clinvar		64
nonsense			9 clinvar			9
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			24 clinvar			24
Total	0	0	104	4	0	108

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032796.4	RefSeq	NP_116185.2	9	MANE Select
ENST00000380155.4	Ensembl	ENSP00000369500.3	9	MANE Select
ENST00000896382.1	Ensembl	ENSP00000566441.1	9	Standard
ENST00000896382.2	Ensembl	ENSP00000566441.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

protein binding

Cellular Component

nucleoplasm
Golgi apparatus
cytosol
cell junction
axon

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380155
Coding exons: 9
Length: 45705
Individuals with no LoFs: 113639
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 113640
p: 0.00000440

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.16	90	127	0.710	0.00000961	2327
Missense (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

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	0.000080	0.000063	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.148

Gene Damage Prediction

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