SYCE3

synaptonemal complex central element protein 3

Basic information

Region (hg38): 22:50551112-50562919

Previous symbols: [ "C22orf41" ]

Links

ENSG00000217442 ∙ NCBI:644186 ∙ OMIM:615775 ∙ HGNC:35245 ∙ Uniprot:A1L190 ∙ 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 SYCE3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYCE3 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			5		1	6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	1

Variants in SYCE3

This is a list of pathogenic ClinVar variants found in the SYCE3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-50551309-T-C		not specified	Uncertain significance (Jun 21, 2021)
22-50551313-C-T			Benign (Jul 01, 2022)
22-50551333-C-T		not specified	Uncertain significance (Mar 02, 2023)
22-50551337-T-C		not specified	Uncertain significance (Sep 20, 2024)
22-50551351-G-A		not specified	Uncertain significance (Apr 18, 2024)
22-50551363-C-T		not specified	Uncertain significance (Mar 03, 2025)
22-50556395-G-A		not specified	Uncertain significance (Dec 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYCE3	protein_coding	protein_coding	ENST00000406915	2	11794

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.600	0.366	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.736	36	50.8	0.709	0.00000290	588
Missense in Polyphen		13	16.743	0.77645		191
Synonymous	0.743	14	18.0	0.777	9.35e-7	144
Loss of Function	1.57	0	2.87	0.00	1.20e-7	43

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Major component of the transverse central element of synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase. Required for chromosome loading of the central element-specific SCS proteins, and for initiating synapsis between homologous chromosomes. Chromosome loading appears to require SYCP1. Required for fertility. {ECO:0000250|UniProtKB:B5KM66}.

Intolerance Scores

• rvis_EVS: 0.77
• rvis_percentile_EVS: 86.89

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syce3
• Phenotype: endocrine/exocrine gland phenotype; reproductive system phenotype

Gene ontology

• Biological process: synaptonemal complex assembly;reciprocal meiotic recombination;spermatogenesis;positive regulation of apoptotic process;cell division
• Cellular component: central element;nucleus;chromosome
• Molecular function: protein binding