SYCE2

protein-coding

synaptonemal complex central element protein 2

Gene summary

The protein encoded by this gene is part of the synaptonemal complex formed between homologous chromosomes during meiotic prophase. The encoded protein associates with SYCP1 and SYCE1 and is found only where chromosome cores are synapsed. [provided by RefSeq, Dec 2012]

MANE transcript

NM_001105578.2

Inheritance

—

ClinVar variants

U:35B:6

Top phenotype

Glutaric aciduria, type 1

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr19:12,898,786-12,919,293

External References & Databases

Ensembl (ENSG00000161860)

Transcript & Mutation Effects

hg38 • Region Span ~20.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SYCE2 variants in ClinVar

5 Conditions Cataloged

Glutaric aciduria, type 1Total: 55

not specifiedTotal: 39

not providedTotal: 16

GCDH-related disorderTotal: 5

Inborn genetic diseasesTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001105578.2. 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	3 clinvar		4
missense			33 clinvar	3 clinvar		36
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	35	6	0	41

Highest pathogenic variant AF is 0.0001239036

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001105578.2	RefSeq	NP_001099048.1	6	MANE Select
ENST00000293695.8	Ensembl	ENSP00000293695.6	6	MANE Select
ENST00000592819.1	Ensembl	ENSP00000466359.1	2	Standard
ENST00000939778.1	Ensembl	ENSP00000609837.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

synaptonemal complex assembly
cell division

Cellular Component

central element
nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000293695
Coding exons: 6
Length: 20491
Individuals with no LoFs: 125720
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125725
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.933	92	121	0.761	0.00000654	1432
Missense (PolyPhen)		24	36.454	0.65837		503
Synonymous	1.13	41	51.3	0.800	0.00000323	395
Loss of Function	2.45	3	12.3	0.244	5.20e-7	144

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0	0.0	absent
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Major component of the transverse central element of synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase. Requires SYCP1 in order to be incorporated into the central element. May have a role in the synaptonemal complex assembly, stabilization and recombination (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.0834

Intolerance Scores

LoFtool: 0.217
RVIS EVS: 0.48
RVIS percentile EVS: 79.04

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.242

Gene Damage Prediction

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