SYCP2L

synaptonemal complex protein 2 like

Basic information

Region (hg38): 6:10886831-10979320

Previous symbols: [ "C6orf177" ]

Links

ENSG00000153157 ∙ NCBI:221711 ∙ OMIM:616799 ∙ HGNC:21537 ∙ Uniprot:Q5T4T6 ∙ 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
Premature ovarian failure 24	AR	Obstetric	Genetic knowledge may be beneficial to allow interventions such as preserving eggs in women with premature ovarian insufficiency	Obstetric	32303603

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SYCP2L gene.

• not_specified (97 variants)
• not_provided (2 variants)
• Premature_ovarian_failure_24 (2 variants)
• See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYCP2L gene is commonly pathogenic or not. These statistics are base on transcript: NM_001040274.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense	1		82	16		99
nonsense		1				1
start loss						0
frameshift	1					1
splice donor/acceptor (+/-2bp)						0
Total	2	1	82	17	0

Highest pathogenic variant AF is 0.000014254

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYCP2L	protein_coding	protein_coding	ENST00000283141	29	231527

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.01e-23	0.0928	124737	0	57	124794	0.000228

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.898	357	408	0.875	0.0000208	5387
Missense in Polyphen		69	95.177	0.72496		1476
Synonymous	0.292	146	151	0.970	0.00000841	1410
Loss of Function	1.56	42	54.4	0.771	0.00000262	687

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000600	0.000593
Ashkenazi Jewish	0.000602	0.000596
East Asian	0.000168	0.000167
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000250	0.000238
Middle Eastern	0.000168	0.000167
South Asian	0.000170	0.000163
Other	0.000336	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Oocyte-specific protein that localizes to centromeres at the dictyate stage and regulates the survival of primordial oocytes. {ECO:0000250|UniProtKB:A0A0M3U1B0}.

Intolerance Scores

• loftool: 0.880
• rvis_EVS: 1.36
• rvis_percentile_EVS: 94.44

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.280
• ghis: 0.393

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0750

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sycp2l
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Cellular component: condensed nuclear chromosome, centromeric region;nucleoplasm