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_specified (34 variants)
not_provided (12 variants)
SYCE1-related_disorder (4 variants)
Spermatogenic_failure_15 (1 variants)
Premature_ovarian_failure_12 (1 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. These statistics are base on transcript: NM_001143764.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar	2 clinvar	6
missense			31 clinvar	3 clinvar	2 clinvar	36
nonsense	1 clinvar					1
start loss						0
frameshift	2 clinvar					2
splice donor/acceptor (+/-2bp)	1 clinvar					1
Total	4	0	31	7	4

Highest pathogenic variant AF is 0.0000334568

Loading clinvar variants...

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

pHI
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