APEX2

apurinic/apyrimidinic endodeoxyribonuclease 2, the group of Zinc fingers GRF-type

Basic information

Region (hg38): X:55000363-55009057

Links

ENSG00000169188 ∙ NCBI:27301 ∙ OMIM:300773 ∙ HGNC:17889 ∙ Uniprot:Q9UBZ4 ∙ 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 APEX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APEX2 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				2	3	5
missense			15	6		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	15	8	3

Variants in APEX2

This is a list of pathogenic ClinVar variants found in the APEX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-55000540-G-C		not specified	Uncertain significance (Jun 03, 2024)
X-55000558-C-T		not specified	Uncertain significance (Mar 20, 2024)
X-55001565-C-T			Benign (Aug 09, 2018)
X-55001609-G-A		not specified	Uncertain significance (May 21, 2024)
X-55001614-C-T		not specified	Uncertain significance (Jul 30, 2024)
X-55002258-C-T			Benign (Dec 31, 2019)
X-55002275-A-G		not specified	Likely benign (Oct 09, 2024)
X-55002323-C-G		not specified	Uncertain significance (Dec 16, 2023)
X-55002349-G-A		not specified	Uncertain significance (Feb 15, 2023)
X-55002382-C-T		not specified	Uncertain significance (Dec 05, 2022)
X-55002385-G-T		not specified	Uncertain significance (May 13, 2022)
X-55002430-C-T			Likely benign (Jul 06, 2018)
X-55002973-G-T		not specified	Uncertain significance (Jun 26, 2024)
X-55003018-C-T		not specified	Uncertain significance (Sep 14, 2023)
X-55003066-G-A		not specified	Uncertain significance (Dec 03, 2024)
X-55003070-G-T		not specified	Uncertain significance (Aug 28, 2023)
X-55003812-C-T			Likely benign (Jan 01, 2023)
X-55003842-A-G		not specified	Uncertain significance (Feb 16, 2023)
X-55006594-A-C		not specified	Uncertain significance (Mar 04, 2024)
X-55006595-T-A		not specified	Uncertain significance (Aug 16, 2022)
X-55006683-C-T			Likely benign (Mar 01, 2023)
X-55006691-C-A		not specified	Uncertain significance (Dec 06, 2021)
X-55006713-G-T		not specified	Uncertain significance (Jan 19, 2024)
X-55006805-A-G			Benign (Jul 03, 2018)
X-55006857-C-T		not specified	Uncertain significance (Apr 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APEX2	protein_coding	protein_coding	ENST00000374987	6	8701

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.973	0.0270	125662	0	3	125665	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.564	177	199	0.888	0.0000161	3365
Missense in Polyphen		39	57.828	0.67442		988
Synonymous	-0.746	85	76.7	1.11	0.00000576	1058
Loss of Function	3.09	0	11.1	0.00	7.74e-7	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000365	0.0000365
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000722	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000122	0.00000880
Middle Eastern	0.0000722	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Function as a weak apurinic/apyrimidinic (AP) endodeoxyribonuclease in the DNA base excision repair (BER) pathway of DNA lesions induced by oxidative and alkylating agents. Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to the damage, generating a single-strand break with 5'-deoxyribose phosphate and 3'-hydroxyl ends. Displays also double-stranded DNA 3'-5' exonuclease, 3'-phosphodiesterase activities. Shows robust 3'-5' exonuclease activity on 3'-recessed heteroduplex DNA and is able to remove mismatched nucleotides preferentially. Shows fairly strong 3'-phosphodiesterase activity involved in the removal of 3'-damaged termini formed in DNA by oxidative agents. In the nucleus functions in the PCNA-dependent BER pathway. Required for somatic hypermutation (SHM) and DNA cleavage step of class switch recombination (CSR) of immunoglobulin genes. Required for proper cell cycle progression during proliferation of peripheral lymphocytes. {ECO:0000269|PubMed:11376153, ECO:0000269|PubMed:16687656, ECO:0000269|PubMed:19443450}.
• Pathway: Base excision repair - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.135

Intolerance Scores

• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.54

Haploinsufficiency Scores

• pHI: 0.0745
• hipred: Y
• hipred_score: 0.831
• ghis: 0.604

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.206

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Apex2
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: base-excision repair;DNA recombination;cell cycle;nucleic acid phosphodiester bond hydrolysis
• Cellular component: fibrillar center;nucleus;mitochondrion;intracellular membrane-bounded organelle
• Molecular function: DNA binding;DNA-(apurinic or apyrimidinic site) endonuclease activity;endonuclease activity;phosphodiesterase I activity;zinc ion binding;double-stranded DNA 3'-5' exodeoxyribonuclease activity;class I DNA-(apurinic or apyrimidinic site) endonuclease activity