SYDE2

synapse defective Rho GTPase homolog 2, the group of C2 domain containing

Basic information

Region (hg38): 1:85156889-85201724

Links

ENSG00000097096 ∙ NCBI:84144 ∙ ∙ HGNC:25841 ∙ Uniprot:Q5VT97 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• multiple congenital anomalies/dysmorphic syndrome (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SYDE2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYDE2 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			48	5	3	56
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	49	6	4

Variants in SYDE2

This is a list of pathogenic ClinVar variants found in the SYDE2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-85159163-G-A			Uncertain significance (Jul 01, 2018)
1-85164532-A-C		not specified	Uncertain significance (Jan 23, 2024)
1-85164586-T-G		not specified	Uncertain significance (Dec 03, 2024)
1-85164624-T-G		not specified	Uncertain significance (Jul 05, 2023)
1-85164633-G-A		not specified	Uncertain significance (Apr 23, 2024)
1-85164672-A-G		not specified	Uncertain significance (Aug 07, 2024)
1-85164745-T-C		not specified	Uncertain significance (Nov 07, 2022)
1-85169123-G-A		not specified	Uncertain significance (Sep 08, 2024)
1-85169127-T-A		not specified	Uncertain significance (Feb 21, 2024)
1-85169217-T-G		not specified	Uncertain significance (Jun 30, 2024)
1-85169220-G-T		not specified	Uncertain significance (Jul 12, 2023)
1-85178142-T-C			Uncertain significance (Jul 01, 2018)
1-85178169-T-A		not specified	Uncertain significance (Mar 28, 2023)
1-85178220-C-T		not specified	Uncertain significance (Aug 04, 2023)
1-85178223-A-G		not specified	Uncertain significance (Sep 04, 2024)
1-85182131-T-G		not specified	Uncertain significance (Jan 26, 2023)
1-85182183-T-C			Uncertain significance (Jul 01, 2019)
1-85182195-A-G		not specified	Uncertain significance (May 24, 2023)
1-85182216-T-C		not specified	Likely benign (Feb 01, 2023)
1-85182235-G-A		not specified	Uncertain significance (Feb 16, 2023)
1-85182258-A-G		not specified	Uncertain significance (Oct 12, 2022)
1-85182416-C-G		not specified	Uncertain significance (Sep 04, 2024)
1-85182538-C-T		not specified	Uncertain significance (Sep 03, 2024)
1-85182543-T-C		not specified	Uncertain significance (Aug 16, 2022)
1-85182547-A-G		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYDE2	protein_coding	protein_coding	ENST00000341460	7	44174

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.31e-17	0.339	124006	2	633	124641	0.00255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.787	531	585	0.908	0.0000278	7763
Missense in Polyphen		184	193.43	0.95123		2745
Synonymous	1.22	193	216	0.894	0.0000103	2340
Loss of Function	1.57	32	43.1	0.742	0.00000263	555

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00132	0.00132
Ashkenazi Jewish	0.00358	0.00358
East Asian	0.00113	0.00111
Finnish	0.0116	0.0116
European (Non-Finnish)	0.00195	0.00193
Middle Eastern	0.00113	0.00111
South Asian	0.00207	0.00203
Other	0.00182	0.00182

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state. {ECO:0000250}.
• Pathway: Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.975
• rvis_EVS: 0.72
• rvis_percentile_EVS: 85.83

Haploinsufficiency Scores

• pHI: 0.381
• hipred: N
• hipred_score: 0.177
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.581

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syde2

Gene ontology

• Biological process: signal transduction;regulation of small GTPase mediated signal transduction;activation of GTPase activity
• Cellular component: cytosol
• Molecular function: GTPase activator activity