SYCE2

synaptonemal complex central element protein 2

Basic information

Region (hg38): 19:12898786-12919293

Links

ENSG00000161860 ∙ NCBI:256126 ∙ OMIM:611487 ∙ HGNC:27411 ∙ Uniprot:Q6PIF2 ∙ 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 SYCE2 gene.

• Glutaric aciduria, type 1 (4 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYCE2 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	4	6	10	22	3	45
Total	4	6	23	24	3

Highest pathogenic variant AF is 0.000263

Variants in SYCE2

This is a list of pathogenic ClinVar variants found in the SYCE2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-12899449-CTG-C		Glutaric aciduria, type 1	Likely benign (May 24, 2023)
19-12899451-G-A		Glutaric aciduria, type 1	Likely benign (Aug 31, 2023)
19-12899451-G-C		Glutaric aciduria, type 1	Likely benign (Nov 17, 2023)
19-12899453-A-G		Glutaric aciduria, type 1	Conflicting classifications of pathogenicity (Jan 08, 2024)
19-12899455-T-C		Glutaric aciduria, type 1	Likely benign (Jul 03, 2023)
19-12899457-A-C		Glutaric aciduria, type 1	Likely benign (Nov 01, 2022)
19-12899458-T-C		Glutaric aciduria, type 1	Likely benign (Aug 20, 2023)
19-12899462-G-A		Glutaric aciduria, type 1	Likely benign (Mar 08, 2022)
19-12899464-C-A		Glutaric aciduria, type 1	Likely benign (Oct 29, 2022)
19-12899464-C-T		Glutaric aciduria, type 1	Likely benign (Aug 20, 2020)
19-12899466-A-C		Glutaric aciduria, type 1	Pathogenic (Mar 05, 2024)
19-12899466-A-G		Glutaric aciduria, type 1	Pathogenic/Likely pathogenic (Feb 26, 2024)
19-12899467-G-A		Glutaric aciduria, type 1	Pathogenic (Jan 29, 2021)
19-12899471-C-T		Glutaric aciduria, type 1	Likely pathogenic (Jun 03, 2021)
19-12899473-C-G		Glutaric aciduria, type 1	Pathogenic (Apr 14, 2022)
19-12899473-C-T		Glutaric aciduria, type 1	Likely pathogenic (Oct 19, 2023)
19-12899475-T-C		Glutaric aciduria, type 1	Likely benign (Oct 29, 2023)
19-12899478-C-T		Glutaric aciduria, type 1	Likely benign (Apr 20, 2023)
19-12899484-C-T		Glutaric aciduria, type 1	Likely benign (Oct 17, 2023)
19-12899485-G-A		Glutaric aciduria, type 1	Pathogenic/Likely pathogenic (Mar 27, 2024)
19-12899486-C-T		Glutaric aciduria, type 1	Pathogenic (Mar 25, 2024)
19-12899490-G-A		Glutaric aciduria, type 1	Likely benign (Mar 04, 2023)
19-12899493-C-T		Glutaric aciduria, type 1	Likely benign (Mar 23, 2021)
19-12899498-G-A		Glutaric aciduria, type 1	Uncertain significance (Aug 30, 2021)
19-12899498-G-T		Glutaric aciduria, type 1	Likely pathogenic (May 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYCE2	protein_coding	protein_coding	ENST00000293695	6	20491

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.281	0.715	125720	0	5	125725	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.933	92	121	0.761	0.00000654	1432
Missense in Polyphen		24	36.454	0.65837		503
Synonymous	1.13	41	51.3	0.800	0.00000323	395
Loss of Function	2.45	3	12.3	0.244	5.20e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Major component of the transverse central element of synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase. Requires SYCP1 in order to be incorporated into the central element. May have a role in the synaptonemal complex assembly, stabilization and recombination (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0834

Intolerance Scores

• loftool: 0.217
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.04

Haploinsufficiency Scores

• pHI: 0.0821
• hipred: N
• hipred_score: 0.273

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.242

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syce2
• Phenotype: endocrine/exocrine gland phenotype; reproductive system phenotype

Gene ontology

• Biological process: synaptonemal complex assembly;cell division
• Cellular component: central element;nucleus