SYCP3 synaptonemal complex protein 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SYCP3provided by HGNC
Official Full Name: synaptonemal complex protein 3provided by HGNC
Primary source: HGNC:HGNC:18130
See related: Ensembl:ENSG00000139351 MIM:604759; AllianceGenome:HGNC:18130
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: COR1; SCP3; SPGF4; RPRGL4
Summary: This gene encodes an essential structural component of the synaptonemal complex. This complex is involved in synapsis, recombination and segregation of meiotic chromosomes. Mutations in this gene are associated with azoospermia in males and susceptibility to pregnancy loss in females. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, May 2010]
Expression: Broad expression in testis (RPKM 35.2), duodenum (RPKM 4.0) and 14 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q23.2

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (101728648..101739462, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (101689875..101700721, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (102122426..102133240, complement)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SCP3 is associated with lymphangiogenesis and provides insight into the SCP3-VEGF-C/VEGF-D axis based cancer therapy strategy.
Title: Synaptonemal complex protein 3 is associated with lymphangiogenesis in non-small cell lung cancer patients with lymph node metastasis.
In the model, the reported compaction of chromosomal DNA caused by SYCP3 would result from its ability to bridge distant sites on a DNA molecule with the DNA-binding domains located at each end of its strut-like structure.
Title: Single-molecule observation of DNA compaction by meiotic protein SYCP3.
SYCP3 binds to RAD51 and attenuates RAD51 activity during meiosis.
Title: SYCP3 regulates strand invasion activities of RAD51 and DMC1.
SYCP3 binding and assembly on meiotic chromosomes leads to their organisation into compact structures compatible with recombination and crossover formation
Title: A molecular model for the role of SYCP3 in meiotic chromosome organisation.
The T657C polymorphism of the SYCP3 gene is possibly associated with recurrent pregnancy loss of unknown cause in human.
Title: The T657C polymorphism on the SYCP3 gene is associated with recurrent pregnancy loss.
SCP3 plays an important role in the progression of cervical cancer
Title: Synaptonemal complex protein 3 is a prognostic marker in cervical cancer.
SYCP3 mutations are not associated with the genetic susceptibility for meiotic arrest in infertile male patients with nonobstructive azoospermia in the Turkish population
Title: Investigation of mutations in the synaptonemal complex protein 3 (SYCP3) gene among azoospermic infertile male patients in the Turkish population.
screening for genetic variants in AURKB and SYCP3 among these patients with reproductive problems using Sanger sequencing. Only one apparently non-pathogenic deletion was found in SYCP3.
Title: Mutation screening of AURKB and SYCP3 in patients with reproductive problems.
Positive synaptonemal complex protein 3 expression is a portent of poor outcome and may be a potential biomarker in the early stages of the non-small cell lung cancer for survival.
Title: Synaptonemal complex protein 3 as a novel prognostic marker in early stage non-small cell lung cancer.
mutations in SYCP3 do not contribute significantly to risk for recurrent miscarriage through maternal meiotic nondisjunction.
Title: Absence of SYCP3 mutations in women with recurrent miscarriage with at least one trisomic miscarriage.

Submit: New GeneRIF Correction See all GeneRIFs (21)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Spermatogenic failure 4 MedGen: C0232981 OMIM: 270960 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH44831 (e-PCR)
- UniSTS:3096

WI-14986 (e-PCR)
- UniSTS:46931

RH77822 (e-PCR)
- UniSTS:7856

SYCP3_9645 (e-PCR)
- UniSTS:468732

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in male meiosis I	NAS Non-traceable Author Statement more info	PubMed
involved_in meiotic cell cycle	IBA Inferred from Biological aspect of Ancestor more info
involved_in sperm DNA condensation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in spermatid development	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in chromosome, centromeric region	ISS Inferred from Sequence or Structural Similarity more info
located_in lateral element	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
is_active_in synaptonemal complex	IBA Inferred from Biological aspect of Ancestor more info
located_in synaptonemal complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: synaptonemal complex protein 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_021181.1 RefSeqGene

Range

5008..15822

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001177948.2 → NP_001171419.1 synaptonemal complex protein 3

See identical proteins and their annotated locations for NP_001171419.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.

Source sequence(s)

AC063950, AF517774

Consensus CDS

CCDS9087.1

UniProtKB/Swiss-Prot

Q8IZU3

Related

ENSP00000266743.2, ENST00000266743.6

Conserved Domains (1) summary

pfam04803
Location:83 → 214

Cor1; Cor1/Xlr/Xmr conserved region
NM_001177949.2 → NP_001171420.1 synaptonemal complex protein 3

See identical proteins and their annotated locations for NP_001171420.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.

Source sequence(s)

AC063950, AF492003, BG201028

Consensus CDS

CCDS9087.1

UniProtKB/Swiss-Prot

Q8IZU3

Related

ENSP00000376655.1, ENST00000392924.2

Conserved Domains (1) summary

pfam04803
Location:83 → 214

Cor1; Cor1/Xlr/Xmr conserved region
NM_153694.5 → NP_710161.1 synaptonemal complex protein 3

See identical proteins and their annotated locations for NP_710161.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.

Source sequence(s)

BC062662, BG202454

Consensus CDS

CCDS9087.1

UniProtKB/Swiss-Prot

Q8IZU3

Related

ENSP00000376658.3, ENST00000392927.7

Conserved Domains (1) summary

pfam04803
Location:83 → 214

Cor1; Cor1/Xlr/Xmr conserved region