SYCE1

synaptonemal complex central element protein 1

Basic information

Region (hg38): 10:133553901-133569835

Previous symbols: [ "C10orf94" ]

Links

ENSG00000171772 ∙ NCBI:93426 ∙ OMIM:611486 ∙ HGNC:28852 ∙ Uniprot:Q8N0S2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Supportive), mode of inheritance: AD
• premature ovarian failure 12 (Strong), mode of inheritance: AR
• spermatogenic failure 15 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Premature ovarian failure 12	AR	Endocrine; Obstetric	The condition can include primary amenorrhea, and hormone therapy has been described as beneficial related to sexual development; Assistive reproductive technologies may be benefiical related to reproduction	Endocrine; Genitourinary; Obstetric	25062452; 25899990; 26203179

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SYCE1 gene.

• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYCE1 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				2	2	4
missense			23	2	4	29
nonsense				1		1
start loss						0
frameshift	2			1		3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding					3	3
Total	2	0	23	6	9

Highest pathogenic variant AF is 0.0000329

Variants in SYCE1

This is a list of pathogenic ClinVar variants found in the SYCE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-133554319-G-C			Benign (Dec 31, 2019)
10-133554332-T-C		SYCE1-related disorder	Likely benign (Dec 06, 2019)
10-133555012-C-T		not specified	Uncertain significance (Jan 23, 2023)
10-133555027-G-T		not specified	Uncertain significance (Jun 17, 2024)
10-133555043-G-A		SYCE1-related disorder	Likely benign (Mar 20, 2019)
10-133555081-C-T		not specified	Uncertain significance (Sep 30, 2024)
10-133555359-C-T		not specified	Uncertain significance (May 23, 2024)
10-133555385-C-T		not specified	Uncertain significance (Aug 05, 2024)
10-133555402-G-C			Benign (Dec 31, 2019)
10-133555414-A-T		not specified	Uncertain significance (Nov 10, 2024)
10-133555644-G-A			Likely benign (Dec 31, 2019)
10-133555649-G-A		not specified	Uncertain significance (May 10, 2022)
10-133555706-G-A		Premature ovarian failure 12	Pathogenic (Jul 15, 2021)
10-133555707-C-T			Likely benign (Oct 01, 2022)
10-133555790-C-A			Benign (Dec 31, 2019)
10-133555801-C-T		not specified	Uncertain significance (May 17, 2023)
10-133555877-C-T		not specified	Uncertain significance (May 04, 2022)
10-133555890-C-G		not specified	Uncertain significance (Jan 07, 2022)
10-133555972-T-C			Benign (Dec 31, 2019)
10-133556037-C-T		not specified	Likely benign (Jun 11, 2024)
10-133556051-AG-A			Benign (Dec 31, 2019)
10-133556759-G-A		SYCE1-related disorder	Likely benign (Apr 11, 2019)
10-133556775-T-A		not specified	Uncertain significance (Apr 22, 2022)
10-133557074-GTC-G			Pathogenic (Jul 25, 2018)
10-133557078-CTGTT-C			Pathogenic (Jun 29, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYCE1	protein_coding	protein_coding	ENST00000343131	13	15473

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.02e-8	0.894	125628	0	119	125747	0.000473

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.663	158	183	0.862	0.00000959	2289
Missense in Polyphen		38	51.757	0.73421		718
Synonymous	0.331	69	72.6	0.951	0.00000390	628
Loss of Function	1.69	15	23.9	0.626	0.00000117	271

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000556	0.000544
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000381	0.000381
Finnish	0.000832	0.000832
European (Non-Finnish)	0.000590	0.000589
Middle Eastern	0.000381	0.000381
South Asian	0.000328	0.000327
Other	0.000491	0.000489

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. {ECO:0000250|UniProtKB:Q9D495}.
• Disease: DISEASE: Premature ovarian failure 12 (POF12) [MIM:616947]: An ovarian disorder defined as the cessation of ovarian function under the age of 40 years. It is characterized by oligomenorrhea or amenorrhea, in the presence of elevated levels of serum gonadotropins and low estradiol. {ECO:0000269|PubMed:25062452}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Spermatogenic failure, 15 (SPGF15) [MIM:616950]: An infertility disorder caused by spermatogenesis defects and characterized by non-obstructive azoospermia due to complete meiotic maturation arrest. SPGF15 inheritance is autosomal recessive. {ECO:0000269|PubMed:25899990}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.0849

Intolerance Scores

• loftool: 0.963
• rvis_EVS: 1.37
• rvis_percentile_EVS: 94.52

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.183
• ghis: 0.392

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0459

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syce1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype

Gene ontology

• Biological process: synaptonemal complex assembly;cell division
• Cellular component: synaptonemal complex;central element
• Molecular function: protein binding