SYCP1

synaptonemal complex protein 1

Basic information

Region (hg38): 1:114854863-114995370

Links

ENSG00000198765 ∙ NCBI:6847 ∙ OMIM:602162 ∙ HGNC:11487 ∙ Uniprot:Q15431 ∙ 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 SYCP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYCP1 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			34	1	1	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	34	1	4

Variants in SYCP1

This is a list of pathogenic ClinVar variants found in the SYCP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-114855565-T-A		not specified	Uncertain significance (Jun 29, 2022)
1-114856580-A-T		not specified	Uncertain significance (May 31, 2023)
1-114856610-C-G		not specified	Uncertain significance (Dec 15, 2022)
1-114856616-C-T		not specified	Uncertain significance (May 26, 2024)
1-114857466-A-G		Mycotic Aneurysm, Intracranial	Conflicting classifications of pathogenicity (Oct 08, 2021)
1-114857483-G-T		not specified	Uncertain significance (Oct 20, 2021)
1-114858570-G-A			Benign (Jun 18, 2018)
1-114858674-T-C		not specified	Uncertain significance (May 18, 2023)
1-114858689-G-A		not specified	Uncertain significance (Aug 10, 2021)
1-114860747-C-T			Benign (Jul 16, 2018)
1-114874508-G-A		not specified	Uncertain significance (Mar 08, 2024)
1-114874517-C-T		not specified	Uncertain significance (Dec 01, 2022)
1-114876088-A-G		not specified	Uncertain significance (Dec 02, 2024)
1-114876128-G-A		not specified	Uncertain significance (Mar 07, 2024)
1-114876129-C-T		not specified	Uncertain significance (Jul 09, 2024)
1-114876763-C-T		not specified	Uncertain significance (Apr 21, 2022)
1-114876794-A-G		not specified	Uncertain significance (Nov 30, 2022)
1-114878131-A-C		not specified	Uncertain significance (Feb 10, 2022)
1-114878169-A-G		not specified	Uncertain significance (Nov 13, 2024)
1-114885560-A-C		not specified	Uncertain significance (Aug 26, 2024)
1-114886173-A-G		not specified	Uncertain significance (Feb 06, 2023)
1-114886240-C-T		not specified	Uncertain significance (Jan 23, 2023)
1-114895480-G-A		not specified	Uncertain significance (Jun 26, 2023)
1-114895489-G-A		not specified	Uncertain significance (Jun 29, 2023)
1-114911486-T-C		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYCP1	protein_coding	protein_coding	ENST00000369522	31	140568

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000346	124581	0	3	124584	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.38	330	408	0.808	0.0000185	6409
Missense in Polyphen		72	125.95	0.57165		2210
Synonymous	-0.367	146	140	1.04	0.00000646	1572
Loss of Function	6.33	7	59.9	0.117	0.00000277	920

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)	0.0000186	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000401	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Major component of the transverse filaments of synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase. Required for normal assembly of the central element of the synaptonemal complexes. Required for normal centromere pairing during meiosis. Required for normal meiotic chromosome synapsis during oocyte and spermatocyte development and for normal male and female fertility. {ECO:0000250|UniProtKB:Q62209}.

Intolerance Scores

• loftool: 0.638
• rvis_EVS: 0.25
• rvis_percentile_EVS: 69.57

Haploinsufficiency Scores

• pHI: 0.0853
• hipred: N
• hipred_score: 0.391

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.135

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sycp1
• Phenotype: endocrine/exocrine gland phenotype; reproductive system phenotype

Gene ontology

• Biological process: meiotic DNA repair synthesis;synapsis;synaptonemal complex assembly;reciprocal meiotic recombination;spermatogenesis;regulation of protein localization;sperm chromatin condensation;chiasma assembly;cell division;lateral element assembly
• Cellular component: chromosome, centromeric region;synaptonemal complex;central element;transverse filament;male germ cell nucleus
• Molecular function: DNA binding