APLF

aprataxin and PNKP like factor, the group of Zinc fingers

Basic information

Region (hg38): 2:68467572-68655862

Previous symbols: [ "C2orf13" ]

Links

ENSG00000169621 ∙ NCBI:200558 ∙ OMIM:611035 ∙ HGNC:28724 ∙ Uniprot:Q8IW19 ∙ 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 APLF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APLF 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			28	2		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	2	0

Variants in APLF

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

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

Position	Type	Phenotype	Significance	ClinVar
2-68467756-C-T		not specified	Uncertain significance (Mar 28, 2024)
2-68467760-G-T		not specified	Uncertain significance (Oct 22, 2021)
2-68467786-G-A		not specified	Uncertain significance (Mar 18, 2024)
2-68467806-C-G		not specified	Uncertain significance (Feb 16, 2023)
2-68490253-A-G		not specified	Uncertain significance (Mar 05, 2024)
2-68502762-C-T		not specified	Uncertain significance (Feb 17, 2024)
2-68502783-C-T		not specified	Uncertain significance (Apr 25, 2022)
2-68502806-T-C		not specified	Uncertain significance (Oct 16, 2023)
2-68502857-C-T		not specified	Likely benign (Oct 05, 2023)
2-68502858-G-A		not specified	Uncertain significance (Dec 12, 2023)
2-68513120-A-T		not specified	Uncertain significance (Dec 12, 2023)
2-68513138-A-T		not specified	Uncertain significance (Jun 12, 2023)
2-68513177-G-A		not specified	Uncertain significance (Oct 04, 2022)
2-68513184-G-T		not specified	Uncertain significance (Jan 16, 2024)
2-68513563-A-G		not specified	Uncertain significance (Sep 01, 2021)
2-68513582-A-G		not specified	Uncertain significance (Aug 01, 2022)
2-68513603-G-A		not specified	Uncertain significance (Sep 01, 2021)
2-68513636-A-G		not specified	Uncertain significance (Mar 13, 2023)
2-68513656-C-G		not specified	Uncertain significance (Sep 07, 2022)
2-68526078-A-G		not specified	Uncertain significance (Feb 28, 2024)
2-68526192-G-A		not specified	Uncertain significance (Sep 22, 2023)
2-68526193-G-A		not specified	Uncertain significance (Nov 08, 2022)
2-68537957-C-T		not specified	Uncertain significance (May 31, 2023)
2-68537961-A-G		not specified	Uncertain significance (May 03, 2023)
2-68538064-G-C		not specified	Uncertain significance (Dec 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APLF	protein_coding	protein_coding	ENST00000303795	10	163312

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.33e-18	0.00146	125571	0	170	125741	0.000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.102	239	243	0.982	0.0000114	3367
Missense in Polyphen		54	57.964	0.93161		876
Synonymous	-0.335	90	86.0	1.05	0.00000422	922
Loss of Function	-0.460	26	23.6	1.10	0.00000107	325

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00177	0.00169
Ashkenazi Jewish	0.00	0.00
East Asian	0.000549	0.000544
Finnish	0.000340	0.000323
European (Non-Finnish)	0.000637	0.000624
Middle Eastern	0.000549	0.000544
South Asian	0.00173	0.00167
Other	0.000336	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Nuclease involved in single-strand and double-strand DNA break repair. Recruited to sites of DNA damage through interaction with poly(ADP-ribose), a polymeric post-translational modification synthesized transiently at sites of chromosomal damage to accelerate DNA strand break repair reactions. Displays apurinic- apyrimidinic (AP) endonuclease and 3'-5' exonuclease activities in vitro. Also able to introduce nicks at hydroxyuracil and other types of pyrimidine base damage. {ECO:0000269|PubMed:17353262, ECO:0000269|PubMed:17396150}.
• Pathway: DNA-PK pathway in nonhomologous end joining (Consensus)

Recessive Scores

• pRec: 0.0732

Intolerance Scores

• loftool: 0.957
• rvis_EVS: 1.07
• rvis_percentile_EVS: 91.61

Haploinsufficiency Scores

• pHI: 0.0577
• hipred: Y
• hipred_score: 0.518
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0121

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Aplf
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: single strand break repair;double-strand break repair;cellular response to DNA damage stimulus;regulation of isotype switching;positive regulation of DNA ligation;nucleic acid phosphodiester bond hydrolysis
• Cellular component: nucleus;nucleoplasm;cytosol;site of double-strand break
• Molecular function: nucleotide binding;DNA-(apurinic or apyrimidinic site) endonuclease activity;endodeoxyribonuclease activity;protein binding;3'-5' exonuclease activity;metal ion binding;class I DNA-(apurinic or apyrimidinic site) endonuclease activity