SDE2

protein-coding

SDE2 telomere maintenance homolog, the group of Spliceosomal C complex|Spliceosomal P complex

Gene summary

Enables damaged DNA binding activity and snoRNA binding activity. Involved in several processes, including cellular response to UV; gene expression; and mitotic G1 DNA damage checkpoint signaling. Located in cytosol; nuclear speck; and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C1orf55

MANE transcript

NM_152608.4

Inheritance

—

ClinVar variants

U:74B:4

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr1:225,982,702-225,999,343

External References & Databases

Ensembl (ENSG00000143751)

Transcript & Mutation Effects

hg38 • Region Span ~16.6 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 SDE2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 73

not providedTotal: 2

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152608.4. 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			71 clinvar	4 clinvar		75
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	74	4	0	78

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152608.4	RefSeq	NP_689821.3	7	MANE Select
ENST00000272091.8	Ensembl	ENSP00000272091.7	7	MANE Select
ENST00000921002.1	Ensembl	ENSP00000591061.1	5	Standard
ENST00000921002.2	Ensembl	ENSP00000591061.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

DNA replication
cell cycle
protein processing
protein ubiquitination
cellular response to UV

Molecular Function

damaged DNA binding
protein binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000272091
Coding exons: 7
Length: 16630
Individuals with no LoFs: 124767
Homozygous LoFs: 0
Heterozygous LoFs: 26
Defined: 124793
p: 0.000104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.209	247	256	0.963	0.0000138	2938
Missense (PolyPhen)		74	98.27	0.75302		1053
Synonymous	-0.265	101	97.7	1.03	0.00000549	877
Loss of Function	1.88	13	22.6	0.574	0.00000138	246

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in both DNA replication and cell cycle control (PubMed:27906959). Unprocessed SDE2 interacts with PCNA via its PIP-box. The interaction with PCNA prevents monoubiquitination of the latter thereby inhibiting translesion DNA synthesis. The binding of SDE2 to PCNA also leads to processing of SDE2 by an unidentified deubiquitinating enzyme, cleaving off the N-terminal ubiquitin-like domain. The resulting mature SDE2 is degraded by the DCX(DTL) complex in a cell cycle- and DNA damage dependent manner (PubMed:27906959). Binding of SDE2 to PCNA is necessary to counteract damage due to ultraviolet light induced replication stress. The complete degradation of SDE2 is necessary to allow S- phase progression (PubMed:27906959). {ECO:0000269|PubMed:27906959}.;

Intolerance Scores

RVIS EVS: 0.06
RVIS percentile EVS: 58.85

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): E

Gene Damage Prediction

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