SYCP2L

protein-coding

synaptonemal complex protein 2 like

Gene summary

Predicted to act upstream of or within negative regulation of programmed cell death. Located in condensed chromosome, centromeric region and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C6orf177

MANE transcript

NM_001040274.3

Inheritance

ClinVar variants

P:5U:95B:17

Top phenotype

Premature ovarian failure 24

gnomAD constraint

pLI —, LoF o/e 0.77

Max pathogenic AF

—

Genomic locus

chr6:10,886,831-10,979,320

External References & Databases

Ensembl (ENSG00000153157)

Transcript & Mutation Effects

hg38 • Region Span ~92.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

premature ovarian failure 24STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0970995

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Premature ovarian failure 24AR

Manifestation: Obstetric

Intervention: Obstetric

Rationale: Genetic knowledge may be beneficial to allow interventions such as preserving eggs in women with premature ovarian insufficiency

Refs: 32303603

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SYCP2L variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 106

Premature ovarian failure 24Total: 5

not providedTotal: 2

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001040274.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense	1 clinvar		94 clinvar	16 clinvar		111
nonsense		1 clinvar				1
start loss						0
frameshift	1 clinvar	1 clinvar				2
splice donor/acceptor (+/-2bp)		1 clinvar	1 clinvar			2
Total	2	3	95	17	0	117

Highest pathogenic variant AF is 0.000014254019

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001040274.3	RefSeq	NP_001035364.2	29	MANE Select
ENST00000283141.11	Ensembl	ENSP00000283141.6	29	MANE Select
ENST00000341041.8	Ensembl	ENSP00000340320.4	12	Standard
ENST00000487561.2	Ensembl	ENSP00000417870.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

condensed nuclear chromosome, centromeric region
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000283141
Coding exons: 29
Length: 231527
Individuals with no LoFs: 124737
Homozygous LoFs: 0
Heterozygous LoFs: 57
Defined: 124794
p: 0.000228

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.898	357	408	0.875	0.0000208	5387
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00039	0.00039	rare
Latino/Admixed American	0.00021	0.00020	rare
Ashkenazi Jewish	0.00060	0.00060	rare
East Asian	0.00017	0.00017	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00025	0.00024	rare
South Asian	0.00017	0.00016	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0750

Gene Damage Prediction

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