SDE2

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

Basic information

Region (hg38): 1:225982702-225999343

Previous symbols: [ "C1orf55" ]

Links

ENSG00000143751 ∙ NCBI:163859 ∙ ∙ HGNC:26643 ∙ Uniprot:Q6IQ49 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SDE2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDE2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			38			38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	0	0

Variants in SDE2

This is a list of pathogenic ClinVar variants found in the SDE2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-225985339-G-C		not specified	Uncertain significance (Jun 09, 2022)
1-225985393-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
1-225985414-C-T		not specified	Uncertain significance (Dec 14, 2023)
1-225985441-C-T		not specified	Uncertain significance (Dec 28, 2024)
1-225985445-T-C		not specified	Uncertain significance (Aug 14, 2024)
1-225985454-C-G		not specified	Uncertain significance (Mar 02, 2023)
1-225985492-G-A		not specified	Uncertain significance (Mar 20, 2024)
1-225985503-T-C		not specified	Uncertain significance (Dec 14, 2023)
1-225987897-G-A		not specified	Uncertain significance (Mar 31, 2023)
1-225987931-C-G		not specified	Uncertain significance (May 30, 2023)
1-225987975-T-C		not specified	Uncertain significance (Nov 03, 2023)
1-225987988-T-C		not specified	Uncertain significance (Dec 18, 2024)
1-225988002-T-G		not specified	Uncertain significance (Sep 02, 2024)
1-225988027-T-C		not specified	Likely benign (Jan 04, 2025)
1-225988069-C-T		not specified	Uncertain significance (Apr 12, 2024)
1-225988152-A-G		not specified	Uncertain significance (Feb 12, 2025)
1-225988176-G-A		not specified	Uncertain significance (Feb 10, 2022)
1-225988201-C-T		not specified	Uncertain significance (Jan 23, 2025)
1-225988248-T-C		not specified	Uncertain significance (Jan 03, 2024)
1-225988269-T-C		not specified	Uncertain significance (May 30, 2024)
1-225988285-G-C		not specified	Uncertain significance (Sep 10, 2024)
1-225988308-G-A		not specified	Uncertain significance (Dec 01, 2022)
1-225988309-T-C		not specified	Uncertain significance (Oct 01, 2024)
1-225991279-T-C		not specified	Uncertain significance (Feb 12, 2025)
1-225991294-G-A		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDE2	protein_coding	protein_coding	ENST00000272091	7	16630

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000124	0.951	124767	0	26	124793	0.000104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.209	247	256	0.963	0.0000138	2938
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000150
Middle Eastern	0.00	0.00
South Asian	0.000165	0.000163
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.144
• ghis: 0.500

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sde2

Gene ontology

• Biological process: DNA replication;cell cycle;protein processing;protein ubiquitination;cellular response to UV;cell division;regulation of cell cycle arrest
• Cellular component: nucleus
• Molecular function: damaged DNA binding;protein binding