SYDE1

synapse defective Rho GTPase homolog 1

Basic information

Region (hg38): 19:15107401-15114985

Links

ENSG00000105137 ∙ NCBI:85360 ∙ OMIM:617377 ∙ HGNC:25824 ∙ Uniprot:Q6ZW31 ∙ 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 SYDE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYDE1 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
missense			57	2		59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	57	2	1

Variants in SYDE1

This is a list of pathogenic ClinVar variants found in the SYDE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-15109071-G-A		not specified	Uncertain significance (Aug 15, 2023)
19-15109097-G-A		not specified	Uncertain significance (Feb 21, 2024)
19-15109127-G-A		not specified	Likely benign (Mar 01, 2023)
19-15109212-G-A		not specified	Uncertain significance (Oct 29, 2024)
19-15109254-T-C		not specified	Uncertain significance (Jan 17, 2025)
19-15109263-G-A		not specified	Uncertain significance (Sep 14, 2021)
19-15109272-G-C		not specified	Uncertain significance (Jun 21, 2022)
19-15109284-C-T		not specified	Uncertain significance (Apr 14, 2023)
19-15109715-G-A		not specified	Uncertain significance (Oct 09, 2024)
19-15109731-A-C		not specified	Uncertain significance (Dec 09, 2023)
19-15109732-A-C		not specified	Uncertain significance (Dec 03, 2024)
19-15109740-G-A		not specified	Uncertain significance (Dec 03, 2024)
19-15109765-G-C		not specified	Uncertain significance (Aug 01, 2024)
19-15109796-G-C		not specified	Uncertain significance (Jan 26, 2023)
19-15109829-C-T		not specified	Uncertain significance (Dec 11, 2024)
19-15109830-G-A		not specified	Uncertain significance (Aug 04, 2023)
19-15109833-C-A		not specified	Uncertain significance (Dec 31, 2024)
19-15109889-C-A		not specified	Uncertain significance (May 16, 2022)
19-15109916-C-A		not specified	Uncertain significance (Sep 22, 2023)
19-15109971-G-A		not specified	Uncertain significance (Jun 11, 2024)
19-15109976-T-C		not specified	Uncertain significance (Aug 20, 2024)
19-15109985-C-T		not specified	Uncertain significance (Dec 05, 2022)
19-15109991-G-T		not specified	Uncertain significance (Nov 18, 2022)
19-15109997-C-T		not specified	Uncertain significance (Nov 15, 2021)
19-15110027-G-A		not specified	Uncertain significance (Jan 16, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYDE1	protein_coding	protein_coding	ENST00000342784	8	7586

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.766	0.234	125727	1	20	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.70	313	410	0.764	0.0000279	4492
Missense in Polyphen		105	162	0.64813		1763
Synonymous	1.88	157	190	0.827	0.0000137	1656
Loss of Function	3.90	5	26.8	0.187	0.00000188	261

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000627	0.0000544
Finnish	0.000190	0.000185
European (Non-Finnish)	0.000116	0.000105
Middle Eastern	0.0000627	0.0000544
South Asian	0.0000328	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase activator for the Rho-type GTPases. As a GCM1 downstream effector, it is involved in placental development and positively regulates trophoblast cells migration. It regulates cytoskeletal remodeling by controlling the activity of Rho GTPases including RHOA, CDC42 and RAC1 (PubMed:27917469). {ECO:0000269|PubMed:27917469}.
• Pathway: Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases (Consensus)

Haploinsufficiency Scores

• pHI: 0.186
• hipred: Y
• hipred_score: 0.662
• ghis: 0.648

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.249

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syde1
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo 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); growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: signal transduction;regulation of small GTPase mediated signal transduction;regulation of cytoskeleton organization;activation of GTPase activity;positive regulation of trophoblast cell migration
• Cellular component: cytosol
• Molecular function: GTPase activator activity