SYCE1L

protein-coding

synaptonemal complex central element protein 1 like

Gene summary

Predicted to be involved in synaptonemal complex assembly. Predicted to be active in synaptonemal complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001129979.3

Inheritance

—

ClinVar variants

U:60B:4

Top phenotype

Non-obstructive azoospermia

gnomAD constraint

pLI —, LoF o/e 1.2

Max pathogenic AF

—

Genomic locus

chr16:77,199,408-77,213,215

External References & Databases

Ensembl (ENSG00000205078)

NCBI Gene (100130958)

Transcript & Mutation Effects

hg38 • Region Span ~13.8 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 SYCE1L variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 60

not providedTotal: 2

Non-obstructive azoospermiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001129979.3. 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			58 clinvar	4 clinvar		62
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	60	4	0	64

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001129979.3	RefSeq	NP_001123451.1	11	MANE Select
ENST00000378644.5	Ensembl	ENSP00000367911.4	11	MANE Select
NM_001348924.2	RefSeq	NP_001335853.1	9	Standard
ENST00000563157.1	Ensembl	ENSP00000454349.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

synaptonemal complex assembly

Cellular Component

synaptonemal complex
intermediate filament cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378644
Coding exons: 11
Length: 13819
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.463	128	114	1.12	0.00000526	1528
Missense (PolyPhen)		32	31.33	1.0214		455
Synonymous	-0.105	46	45.1	1.02	0.00000218	438
Loss of Function	-0.751	19	15.8	1.20	7.69e-7	200

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	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in meiosis. {ECO:0000250}.;

Intolerance Scores

RVIS EVS: 0.72
RVIS percentile EVS: 85.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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