SYCE1L

synaptonemal complex central element protein 1 like

Basic information

Region (hg38): 16:77199408-77213215

Links

ENSG00000205078 ∙ NCBI:100130958 ∙ OMIM:619954 ∙ HGNC:37236 ∙ Uniprot:A8MT33 ∙ 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 SYCE1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYCE1L 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			32	3		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	32	3	0

Variants in SYCE1L

This is a list of pathogenic ClinVar variants found in the SYCE1L region.

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

Position	Type	Phenotype	Significance	ClinVar
16-77199455-G-A		not specified	Uncertain significance (Jan 17, 2023)
16-77199456-C-T		not specified	Uncertain significance (Aug 27, 2024)
16-77199470-C-T		not specified	Uncertain significance (Aug 28, 2024)
16-77199473-C-G		Non-obstructive azoospermia	Benign/Likely benign (Jun 07, 2020)
16-77199489-C-T		not specified	Uncertain significance (Jan 10, 2022)
16-77206482-G-A		not specified	Uncertain significance (Jul 27, 2021)
16-77206496-G-T		not specified	Uncertain significance (Jul 10, 2024)
16-77208211-G-C		not specified	Uncertain significance (Dec 23, 2024)
16-77208223-G-T		not specified	Uncertain significance (Dec 04, 2024)
16-77208238-C-A		not specified	Uncertain significance (Jan 17, 2025)
16-77208240-T-C		not specified	Uncertain significance (Aug 16, 2022)
16-77208249-G-A		not specified	Uncertain significance (Mar 31, 2024)
16-77208480-G-A		not specified	Uncertain significance (Oct 14, 2023)
16-77208491-A-G		not specified	Likely benign (May 23, 2024)
16-77208506-C-G		not specified	Uncertain significance (Jan 08, 2025)
16-77208519-T-C		not specified	Uncertain significance (Aug 04, 2023)
16-77208526-G-C		not specified	Uncertain significance (Feb 04, 2025)
16-77208537-C-T		not specified	Uncertain significance (Jun 26, 2023)
16-77209137-A-T		not specified	Uncertain significance (Dec 28, 2023)
16-77209440-C-T		not specified	Uncertain significance (Nov 15, 2021)
16-77211244-A-G		not specified	Uncertain significance (Nov 12, 2021)
16-77211246-G-A		not specified	Uncertain significance (Sep 06, 2022)
16-77211271-T-C		not specified	Uncertain significance (Jun 26, 2024)
16-77212184-C-A		not specified	Uncertain significance (Nov 18, 2022)
16-77212191-T-A		not specified	Uncertain significance (May 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYCE1L	protein_coding	protein_coding	ENST00000378644	11	13819

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.43e-14	0.00480	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.463	128	114	1.12	0.00000526	1528
Missense in Polyphen		32	31.33	1.0214		455
Synonymous	-0.105	46	45.1	1.02	0.00000218	438
Loss of Function	-0.751	19	15.8	1.20	7.69e-7	200

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: May be involved in meiosis. {ECO:0000250}.

Intolerance Scores

• rvis_EVS: 0.72
• rvis_percentile_EVS: 85.92

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

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	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Syce1l

Gene ontology

• Biological process: synaptonemal complex assembly
• Cellular component: synaptonemal complex;intermediate filament cytoskeleton