SYCP3

synaptonemal complex protein 3

Basic information

Region (hg38): 12:101728648-101739472

Links

ENSG00000139351 ∙ NCBI:50511 ∙ OMIM:604759 ∙ HGNC:18130 ∙ Uniprot:Q8IZU3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 4; Pregnancy loss, recurrent, 4	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary; Obstetric	14643120; 19110213

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SYCP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYCP3 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
missense			13	1	1	15
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4	1	13	18
Total	0	0	19	2	16

Variants in SYCP3

This is a list of pathogenic ClinVar variants found in the SYCP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-101728682-TAGAG-T		Spermatogenic Failure	Likely benign (Jun 14, 2016)
12-101728684-G-C		Spermatogenic failure 4	Uncertain significance (Jan 12, 2018)
12-101728722-C-T		Spermatogenic failure 4	Benign (Jan 12, 2018)
12-101728729-C-T		Spermatogenic failure 4	Uncertain significance (Jan 13, 2018)
12-101728744-T-C		Spermatogenic failure 4	Benign (Jan 12, 2018)
12-101728962-T-C		not specified	Uncertain significance (Aug 30, 2022)
12-101728972-T-C		Spermatogenic failure 4	Benign (Sep 10, 2018)
12-101728973-T-A		not specified	Uncertain significance (Aug 02, 2023)
12-101729109-A-G		Spermatogenic failure 4	Pathogenic (Jan 01, 2009)
12-101729122-AT-A		Spermatogenic failure 4	Pathogenic (Nov 22, 2003)
12-101729168-C-T		not specified	Uncertain significance (Dec 19, 2023)
12-101729177-G-A		not specified	Uncertain significance (Jun 30, 2023)
12-101729212-C-T		not specified	Uncertain significance (Mar 21, 2023)
12-101729230-CAAGT-C		Spermatogenic failure 4	Pathogenic (Jan 01, 2009)
12-101729443-C-A			Benign (Nov 12, 2018)
12-101731312-G-A			Benign (Nov 12, 2018)
12-101731592-TTTAA-T		Spermatogenic failure 4	Uncertain significance (Oct 15, 2018)
12-101731624-T-G		not specified	Uncertain significance (May 15, 2023)
12-101731636-G-A		Spermatogenic failure 4	Uncertain significance (Nov 15, 2023)
12-101731674-TATAAA-T		Spermatogenic Failure	Benign (Nov 12, 2018)
12-101733484-C-A			Benign (Nov 12, 2018)
12-101733593-T-C		Spermatogenic failure 4	Benign (Dec 31, 2019)
12-101733936-T-G			Benign (Nov 12, 2018)
12-101734989-C-G		not specified	Uncertain significance (Jan 09, 2023)
12-101735039-T-G		Male infertility	Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYCP3	protein_coding	protein_coding	ENST00000392927	8	10825

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000918	0.941	125715	0	31	125746	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.536	102	118	0.861	0.00000573	1590
Missense in Polyphen		10	20.408	0.48999		325
Synonymous	-0.187	38	36.6	1.04	0.00000183	370
Loss of Function	1.72	9	16.5	0.544	7.63e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000213	0.000211
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000664	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase. Required for centromere pairing during meiosis in male germ cells (By similarity). Required for normal meiosis during spermatogenesis and male fertility (PubMed:14643120). Plays a lesser role in female fertility. Required for efficient phosphorylation of HORMAD1 and HORMAD2 (By similarity). {ECO:0000250|UniProtKB:P70281, ECO:0000269|PubMed:14643120}.
• Disease: DISEASE: Spermatogenic failure 4 (SPGF4) [MIM:270960]: An infertility disorder characterized by azoospermia, a condition of having no sperm present in the ejaculate. Testicular histology shows arrest of spermatogenesis at the pachytene stage of primary spermatocytes. {ECO:0000269|PubMed:14643120}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Pregnancy loss, recurrent, 4 (RPRGL4) [MIM:270960]: A common complication of pregnancy, resulting in spontaneous abortion before the fetus has reached viability. The term includes all miscarriages from the time of conception until 24 weeks of gestation. Recurrent pregnancy loss is defined as 3 or more consecutive spontaneous abortions. {ECO:0000269|PubMed:19110213}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
• Pathway: Homologous recombination - Homo sapiens (human);Reproduction;Meiotic synapsis;Meiosis;Cell Cycle (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.374
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.130
• hipred: N
• hipred_score: 0.438
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.835

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sycp3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: male meiosis I;spermatogenesis;spermatid development;spermatogenesis, exchange of chromosomal proteins;cell division;meiotic cell cycle
• Cellular component: chromosome, centromeric region;synaptonemal complex;lateral element;nucleus
• Molecular function: DNA binding