SYCP2

synaptonemal complex protein 2

Basic information

Region (hg38): 20:59863564-59933655

Links

ENSG00000196074 ∙ NCBI:10388 ∙ OMIM:604105 ∙ HGNC:11490 ∙ Uniprot:Q9BX26 ∙ 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 1	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	Endocrine; Genitourinary	31866047

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SYCP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYCP2 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				4	3	7
missense			72	4	6	82
nonsense						0
start loss						0
frameshift		3				3
inframe indel						0
splice donor/acceptor (+/-2bp)		2				2
splice region				1		1
non coding						0
Total	0	5	72	8	9

Variants in SYCP2

This is a list of pathogenic ClinVar variants found in the SYCP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-59864330-T-A		not specified	Uncertain significance (Apr 12, 2024)
20-59864336-G-A		not specified	Uncertain significance (Mar 16, 2022)
20-59864340-T-C		not specified	Uncertain significance (Jun 11, 2021)
20-59865441-A-G		not specified	Uncertain significance (Mar 05, 2024)
20-59865590-T-C		not specified	Uncertain significance (Aug 26, 2022)
20-59865626-C-T		not specified	Uncertain significance (Jan 24, 2024)
20-59865818-G-A		SYCP2-related disorder	Likely benign (Mar 01, 2023)
20-59866317-T-A		not specified	Uncertain significance (Sep 25, 2024)
20-59866364-T-A		not specified	Uncertain significance (Jan 24, 2024)
20-59866365-G-A			Likely benign (Feb 01, 2023)
20-59866509-T-G		not specified	Uncertain significance (Sep 22, 2022)
20-59866557-C-T			Benign (Aug 16, 2018)
20-59867718-C-T		not specified	Likely benign (Aug 11, 2024)
20-59867788-G-T		not specified	Uncertain significance (Sep 28, 2022)
20-59867813-G-A			Benign (Aug 15, 2018)
20-59867826-A-G		not specified	Uncertain significance (Apr 23, 2024)
20-59867833-A-G		not specified	Uncertain significance (Jan 24, 2024)
20-59868431-C-G		not specified	Uncertain significance (Jul 11, 2023)
20-59868460-G-A		not specified	Uncertain significance (Nov 14, 2024)
20-59868523-T-C		not specified	Uncertain significance (Aug 26, 2024)
20-59868538-A-C		not specified	Uncertain significance (Mar 23, 2022)
20-59868547-C-T		not specified	Uncertain significance (Mar 29, 2023)
20-59868559-T-A		not specified	Uncertain significance (Apr 16, 2024)
20-59868890-A-C		not specified	Uncertain significance (Mar 28, 2024)
20-59869895-T-C		not specified	Uncertain significance (Mar 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYCP2	protein_coding	protein_coding	ENST00000357552	43	70093

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	5.45e-8	125675	0	34	125709	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.258	691	710	0.973	0.0000340	10180
Missense in Polyphen		144	188.15	0.76535		2942
Synonymous	-0.507	246	236	1.04	0.0000118	2576
Loss of Function	7.69	9	86.0	0.105	0.00000411	1226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000220	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000250	0.000237
Middle Eastern	0.000220	0.000217
South Asian	0.0000677	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Major component of the axial/lateral elements of synaptonemal complexes (SCS) during meiotic prophase. Plays a role in the assembly of synaptonemal complexes. Required for normal meiotic chromosome synapsis during oocyte and spermatocyte development and for normal male and female fertility. Required for insertion of SYCP3 into synaptonemal complexes. May be involved in the organization of chromatin by temporarily binding to DNA scaffold attachment regions. Requires SYCP3, but not SYCP1, in order to be incorporated into the axial/lateral elements. {ECO:0000250|UniProtKB:Q9CUU3}.
• Pathway: Reproduction;Meiotic synapsis;Meiosis;Cell Cycle (Consensus)

Recessive Scores

• pRec: 0.401

Intolerance Scores

• loftool: 0.557
• rvis_EVS: 0.92
• rvis_percentile_EVS: 89.58

Haploinsufficiency Scores

• pHI: 0.129
• hipred: Y
• hipred_score: 0.621
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.163

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sycp2
• Phenotype: reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: synaptonemal complex assembly;male meiotic nuclear division;female meiotic nuclear division;fertilization;negative regulation of apoptotic process;male genitalia morphogenesis;cell division
• Cellular component: synaptonemal complex;lateral element;nucleus
• Molecular function: DNA binding;protein heterodimerization activity