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SYCP2L

gene
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Also known as dJ62D2.1NO145

Summary

SYCP2L (synaptonemal complex protein 2 like, HGNC:21537) is a protein-coding gene on chromosome 6p24.2, encoding Synaptonemal complex protein 2-like (Q5T4T6). Oocyte-specific protein that localizes to centromeres at the dictyate stage and regulates the survival of primordial oocytes.

Predicted to act upstream of or within negative regulation of programmed cell death. Located in condensed chromosome, centromeric region and nucleoplasm.

Source: NCBI Gene 221711 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): premature ovarian failure 24 (Strong, GenCC)
  • GWAS associations: 17
  • Clinical variants (ClinVar): 118 total — 2 pathogenic, 1 likely-pathogenic
  • Phenotypes (HPO): 10
  • MANE Select transcript: NM_001040274

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:21537
Approved symbolSYCP2L
Namesynaptonemal complex protein 2 like
Location6p24.2
Locus typegene with protein product
StatusApproved
AliasesdJ62D2.1, NO145
Ensembl geneENSG00000153157
Ensembl biotypeprotein_coding
OMIM616799
Entrez221711

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 protein_coding, 1 retained_intron

ENST00000283141, ENST00000341041, ENST00000465872, ENST00000474197, ENST00000487561, ENST00000488191

RefSeq mRNA: 1 — MANE Select: NM_001040274 NM_001040274

CCDS: CCDS43423

Canonical transcript exons

ENST00000283141 — 30 exons

ExonStartEnd
ENSE000019209781097395210974309
ENSE000034714511095878410958875
ENSE000034798941096130510961404
ENSE000034833631092633910926432
ENSE000035153711092449610924641
ENSE000035180661096378210963843
ENSE000035226681091082410910869
ENSE000035250541096150010961558
ENSE000035261751091286710912927
ENSE000035295741091014810910200
ENSE000035594411095511610955217
ENSE000035723281090754210907684
ENSE000035791131089151310891581
ENSE000035902371090602010906054
ENSE000036112111094245910942529
ENSE000036254451092724010927367
ENSE000036272801093505810935187
ENSE000036449491090287510902963
ENSE000036506031093037010930514
ENSE000036525211094267710942746
ENSE000036529811093144010931489
ENSE000036741341091267310912765
ENSE000036780011095613610956242
ENSE000036837641092840310928450
ENSE000037152191089408510894204
ENSE000037215741090267710902762
ENSE000037304171089882410898848
ENSE000037320751089386710894004
ENSE000037351351089801110898115
ENSE000038485481088705210887135

Expression profiles

Bgee: expression breadth ubiquitous, 161 present calls, max score 86.90.

FANTOM5 (CAGE): breadth broad, TPM avg 1.3590 / max 75.1611, expressed in 321 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
657851.3590321

Top tissues by expression

244 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047386.90gold quality
secondary oocyteCL:000065580.30gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099179.90gold quality
sural nerveUBERON:001548875.40gold quality
cerebellar hemisphereUBERON:000224574.52gold quality
cerebellar cortexUBERON:000212974.34gold quality
right hemisphere of cerebellumUBERON:001489073.78gold quality
right testisUBERON:000453472.84gold quality
left testisUBERON:000453372.55gold quality
testisUBERON:000047372.22gold quality
cerebellumUBERON:000203771.74gold quality
Brodmann (1909) area 9UBERON:001354071.63gold quality
cortical plateUBERON:000534371.29gold quality
mucosa of stomachUBERON:000119970.64gold quality
right frontal lobeUBERON:000281070.51gold quality
body of pancreasUBERON:000115070.45gold quality
oocyteCL:000002370.42gold quality
calcaneal tendonUBERON:000370170.25gold quality
upper lobe of left lungUBERON:000895268.36gold quality
ventricular zoneUBERON:000305368.19gold quality
tibial nerveUBERON:000132368.03gold quality
anterior cingulate cortexUBERON:000983567.81gold quality
right lungUBERON:000216767.39gold quality
upper lobe of lungUBERON:000894866.91gold quality
granulocyteCL:000009466.28gold quality
ganglionic eminenceUBERON:000402366.20gold quality
dorsolateral prefrontal cortexUBERON:000983465.53gold quality
apex of heartUBERON:000209865.42gold quality
C1 segment of cervical spinal cordUBERON:000646965.37gold quality
left lobe of thyroid glandUBERON:000112065.03gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no4.90
E-MTAB-6678no2.42

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 3)

  • We find that a human SYCP2L intronic single nucleotide polymorphism (SNP) rs2153157, which is associated with ANM, changes the splicing efficiency of U12-type minor introns (PMID:26362258)
  • Homozygous variants in SYCP2L cause premature ovarian insufficiency. (PMID:32303603)
  • Involvement of SYCP2L and TDRD3 gene variants on ovarian reserve and reproductive outcomes: a cross-sectional study. (PMID:37417852)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusSycp2lENSMUSG00000038651
rattus_norvegicusSycp2lENSRNOG00000023831

Paralogs (1): SYCP2 (ENSG00000196074)

Protein

Protein identifiers

Synaptonemal complex protein 2-like — Q5T4T6 (reviewed: Q5T4T6)

Alternative names: 145 kDa nucleolar protein homolog

All UniProt accessions (2): Q5T4T6, H7C4Q1

UniProt curated annotations — full annotation on UniProt →

Function. Oocyte-specific protein that localizes to centromeres at the dictyate stage and regulates the survival of primordial oocytes.

Subcellular location. Nucleus. Chromosome. Centromere.

Tissue specificity. Expressed in the ovary (at protein level). In the ovaries, expressed in oocytes, including germinal vesicle oocytes, metaphase I and metaphase II oocytes. Also expressed in testis.

Disease relevance. Premature ovarian failure 24 (POF24) [MIM:620840] A form of premature ovarian failure, an ovarian disorder defined as the cessation of ovarian function under the age of 40 years. It is characterized by oligomenorrhea or amenorrhea, in the presence of elevated levels of serum gonadotropins and low estradiol. POF24 inheritance is autosomal recessive. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the SYCP2 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q5T4T6-11yes
Q5T4T6-22

RefSeq proteins (1): NP_001035364* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR024835SYCP2-likeFamily
IPR040560SYCP2_SLDDomain
IPR041322SYCP2_ARLDDomain

Pfam: PF18581, PF18584

UniProt features (20 total): sequence variant 7, compositionally biased region 6, sequence conflict 3, region of interest 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5T4T6-F166.450.35

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 80 (showing top): AGGAAGC_MIR5163P, chr6p24, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, GOCC_CHROMOSOMAL_REGION, GOCC_CONDENSED_CHROMOSOME_CENTROMERIC_REGION, GOCC_LATERAL_ELEMENT, GOCC_NUCLEAR_CHROMOSOME, GOCC_CONDENSED_NUCLEAR_CHROMOSOME, WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_UP, GOCC_SYNAPTONEMAL_STRUCTURE, BCL6B_TARGET_GENES, HSD17B8_TARGET_GENES, ZFP91_TARGET_GENES, ZNF30_TARGET_GENES, MIR655_3P

GO Biological Process (1): negative regulation of programmed cell death (GO:0043069)

GO Molecular Function (0):

GO Cellular Component (7): condensed chromosome, centromeric region (GO:0000779), lateral element (GO:0000800), female germ cell nucleus (GO:0001674), nucleoplasm (GO:0005654), chromosome, centromeric region (GO:0000775), nucleus (GO:0005634), chromosome (GO:0005694)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
programmed cell death1
regulation of programmed cell death1
negative regulation of cellular process1
chromosome, centromeric region1
condensed chromosome1
synaptonemal complex1
germ cell nucleus1
nuclear lumen1
chromosomal region1
intracellular membrane-bounded organelle1
intracellular membraneless organelle1

Protein interactions and networks

STRING

288 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SYCP2LTMEM150BA6NC51610
SYCP2LSCP2P22307598
SYCP2LMCM8Q9UJA3593
SYCP2LELOVL2Q9NXB9544
SYCP2LTMEM200CA6NKL6541
SYCP2LA0A494C100A0A494C100513
SYCP2LBRSK1Q8TDC3506
SYCP2LHK3P52790479
SYCP2LUIMC1Q96RL1479
SYCP2LELOVL5Q9NYP7474
SYCP2LHSDL2Q6YN16419
SYCP2LHSD17B4P51659418
SYCP2LZSCAN12O43309417
SYCP2LNDUFS5O43920385
SYCP2LMTHFSDQ2M296357

IntAct

4 interactions, top by confidence:

ABTypeScore
SYCP2LCCT2psi-mi:“MI:0915”(physical association)0.400
SYCP2LPARP1psi-mi:“MI:0915”(physical association)0.400
SYCP2Lpsi-mi:“MI:0915”(physical association)0.000

BioGRID (7): SYCP2L (Two-hybrid), SYCP2L (Proximity Label-MS), SYCP2L (Proximity Label-MS), SYCP2L (Affinity Capture-MS), SYCP2L (Cross-Linking-MS (XL-MS)), SYCP2L (Affinity Capture-RNA), APP (Reconstituted Complex)

ESM2 similar proteins: A0A0M3U1B0, A0A1L8EYB2, A0JMF7, A1L2Y1, A2ALV5, A9JRX0, B2GUZ2, D3ZSP7, F1QB81, O35892, O70608, O75113, P23497, P70347, Q0P5X5, Q13129, Q16533, Q2T9I9, Q3U1D0, Q5CZC0, Q5H9M0, Q5REF4, Q5RHB5, Q5SW75, Q5T4T6, Q5T5J6, Q5XG69, Q5ZLE9, Q60664, Q63HN8, Q7M6U3, Q7Z4H7, Q80VH0, Q8BVK9, Q8C263, Q8CCC3, Q8NA03, Q90WN7, Q92844, Q96QP1

Diamond homologs: A0A0M3U1B0, O70608, Q5T4T6, Q90WN7, Q9BX26, Q9CUU3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

118 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic2
Likely pathogenic1
Uncertain significance74
Likely benign15
Benign0

Top pathogenic / likely-pathogenic (3)

Variant IDHGVSClassification
3237150NM_001040274.3(SYCP2L):c.154_155del (p.Ser52fs)Pathogenic
3237151NM_001040274.3(SYCP2L):c.999A>G (p.Ile333Met)Pathogenic
2681144NM_001040274.3(SYCP2L):c.1528C>T (p.Gln510Ter)Likely pathogenic

SpliceAI

5236 predictions. Top by Δscore:

VariantEffectΔscore
6:10887132:AGCG:Adonor_gain1.0000
6:10887132:AGCGG:Adonor_loss1.0000
6:10887133:GCG:Gdonor_gain1.0000
6:10887133:GCGG:Gdonor_gain1.0000
6:10887133:GCGGT:Gdonor_loss1.0000
6:10887134:CGGTG:Cdonor_loss1.0000
6:10887135:GGT:Gdonor_loss1.0000
6:10887136:G:GGdonor_gain1.0000
6:10887137:T:Adonor_loss1.0000
6:10888576:G:GTdonor_gain1.0000
6:10891507:A:AGacceptor_gain1.0000
6:10891508:C:Gacceptor_gain1.0000
6:10891508:CACA:Cacceptor_loss1.0000
6:10891509:A:AGacceptor_gain1.0000
6:10891509:ACAG:Aacceptor_loss1.0000
6:10891510:C:Gacceptor_gain1.0000
6:10891510:CAGA:Cacceptor_loss1.0000
6:10891511:A:AGacceptor_gain1.0000
6:10891512:G:GAacceptor_gain1.0000
6:10891512:G:Tacceptor_loss1.0000
6:10891512:GA:Gacceptor_gain1.0000
6:10891512:GAA:Gacceptor_gain1.0000
6:10891512:GAAA:Gacceptor_gain1.0000
6:10891512:GAAAA:Gacceptor_gain1.0000
6:10891580:GG:Gdonor_gain1.0000
6:10891581:GG:Gdonor_gain1.0000
6:10891581:GGT:Gdonor_loss1.0000
6:10891582:G:GGdonor_gain1.0000
6:10891583:T:Adonor_loss1.0000
6:10893862:TCCA:Tacceptor_loss1.0000

AlphaMissense

5415 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:10912709:T:AW319R0.991
6:10912709:T:CW319R0.991
6:10907622:T:AW253R0.988
6:10907622:T:CW253R0.988
6:10910842:T:GC297W0.988
6:10910156:A:CR276S0.987
6:10910156:A:TR276S0.987
6:10910173:T:CL282P0.986
6:10910840:T:CC297R0.985
6:10912706:T:CF318L0.983
6:10912708:T:AF318L0.983
6:10912708:T:GF318L0.983
6:10910161:T:CF278S0.982
6:10910850:C:AA300D0.982
6:10910155:G:CR276T0.981
6:10910160:T:CF278L0.980
6:10910162:T:AF278L0.980
6:10910162:T:GF278L0.980
6:10907676:T:CF271L0.979
6:10907678:T:AF271L0.979
6:10907678:T:GF271L0.979
6:10912740:T:AV329D0.976
6:10907625:T:CF254L0.975
6:10907627:T:AF254L0.975
6:10907627:T:GF254L0.975
6:10924582:T:CF387L0.975
6:10924584:T:AF387L0.975
6:10924584:T:GF387L0.975
6:10910852:T:CF301L0.974
6:10910854:T:AF301L0.974

dbSNP variants (sampled 300 via entrez): RS1000010719 (6:10906283 G>A), RS1000039077 (6:10959724 C>G), RS1000052587 (6:10945963 T>C), RS1000064583 (6:10906622 A>C,T), RS1000159413 (6:10929034 G>A), RS1000209053 (6:10939516 A>G), RS1000235013 (6:10971393 G>A), RS1000269274 (6:10923079 G>A), RS1000281745 (6:10895700 C>T), RS1000294272 (6:10901648 C>T), RS1000296288 (6:10928679 C>T), RS1000338699 (6:10962934 C>T), RS1000339516 (6:10934807 A>G), RS1000418867 (6:10964999 G>A), RS1000426383 (6:10923250 G>A)

Disease associations

OMIM: gene MIM:616799 | disease phenotypes: MIM:620840

GenCC curated gene-disease

DiseaseClassificationInheritance
premature ovarian failure 24StrongAutosomal recessive

Mondo (1): premature ovarian failure 24 (MONDO:0970995)

Orphanet (0):

HPO phenotypes

10 total (10 of 10 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000869Secondary amenorrhea
HP:0000876Oligomenorrhea
HP:0008214Decreased serum estradiol
HP:0008222Female infertility
HP:0008232Elevated circulating follicle stimulating hormone level
HP:0011462Young adult onset
HP:0011969Elevated circulating luteinizing hormone level
HP:0031103Decreased circulating antimullerian hormone circulation
HP:0033085Reduced antral follicle count

GWAS associations

17 associations (top):

StudyTraitp-value
GCST000403_2Menarche and menopause (age at onset)5.000000e-08
GCST001177_3Plasma omega-3 polyunsaturated fatty acid levels (docosahexaenoic acid)8.000000e-14
GCST001178_13Plasma omega-3 polyunsaturated fatty acid level (eicosapentaenoic acid)3.000000e-08
GCST001179_2Plasma omega-3 polyunsaturated fatty acid levels (docosapentaenoic acid)3.000000e-36
GCST001381_16Menopause (age at onset)8.000000e-12
GCST002550_6Allergic rhinitis6.000000e-07
GCST002712_5Red blood cell fatty acid levels4.000000e-09
GCST002830_21Urate levels in lean individuals8.000000e-06
GCST003830_22Response to bronchodilator in chronic obstructive pulmonary disease (change in FEV1)3.000000e-07
GCST003830_37Response to bronchodilator in chronic obstructive pulmonary disease (change in FEV1)1.000000e-07
GCST003830_9Response to bronchodilator in chronic obstructive pulmonary disease (change in FEV1)5.000000e-07
GCST004227_11Obstetric antiphospholipid syndrome2.000000e-06
GCST004227_4Obstetric antiphospholipid syndrome1.000000e-06
GCST005312_18Menopause (age at onset)2.000000e-19
GCST005312_47Menopause (age at onset)4.000000e-13
GCST009172_2Response to (pegylated) interferon in HBeAg-negative hepatitis B3.000000e-06
GCST010105_172Nicotine dependence symptom count5.000000e-06

EFO canonical traits (8, from GWAS)

EFO IDTrait name
EFO:0004704age at menopause
EFO:0007761docosahexaenoic acid measurement
EFO:0007760eicosapentaenoic acid measurement
EFO:0006809docosapentaenoic acid measurement
EFO:0004531urate measurement
EFO:0005921FEV change measurement
EFO:0007859response to interferon
EFO:0009262nicotine dependence symptom count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression, increases expression3
trichostatin Aincreases expression1
butyraldehydedecreases expression1
hydroquinonedecreases expression1
pinostrobinincreases expression1
bisphenol Saffects cotreatment, increases methylation1
(+)-JQ1 compoundincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Air Pollutantsdecreases expression1
Benzo(a)pyreneincreases methylation1
Cisplatindecreases expression1
Smokedecreases expression1
Aflatoxin B1increases methylation1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
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BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot