APOBEC4

apolipoprotein B mRNA editing enzyme catalytic polypeptide like 4, the group of Apolipoprotein B mRNA editing enzyme catalytic subunits

Basic information

Region (hg38): 1:183646274-183653316

Previous symbols: [ "C1orf169" ]

Links

ENSG00000173627 ∙ NCBI:403314 ∙ OMIM:609908 ∙ HGNC:32152 ∙ Uniprot:Q8WW27 ∙ 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 APOBEC4 gene.

• Inborn genetic diseases (7 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOBEC4 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					1	1
missense			6	1	3	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	4

Variants in APOBEC4

This is a list of pathogenic ClinVar variants found in the APOBEC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-183647716-C-T		not specified	Uncertain significance (Jan 22, 2024)
1-183647821-T-C			Benign (Dec 31, 2019)
1-183647883-T-C			Benign (Dec 31, 2019)
1-183647916-G-A		not specified	Likely benign (Aug 02, 2023)
1-183648079-C-T		not specified	Uncertain significance (Aug 08, 2022)
1-183648102-T-C		not specified	Uncertain significance (Dec 21, 2023)
1-183648172-C-T		not specified	Uncertain significance (Dec 13, 2022)
1-183648195-G-C			Benign (Dec 31, 2019)
1-183648236-C-T			Benign (Apr 30, 2018)
1-183648259-G-A		not specified	Uncertain significance (Dec 06, 2021)
1-183648268-C-T		not specified	Uncertain significance (Dec 16, 2021)
1-183648499-C-T		not specified	Uncertain significance (Oct 16, 2023)
1-183648609-G-A		not specified	Uncertain significance (Oct 06, 2023)
1-183648675-C-A		not specified	Uncertain significance (Apr 04, 2023)
1-183648690-C-A		not specified	Uncertain significance (Apr 19, 2023)
1-183648703-C-T		not specified	Uncertain significance (Jan 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOBEC4	protein_coding	protein_coding	ENST00000308641	1	6911

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000817	0.548	125697	0	50	125747	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.557	173	195	0.888	0.00000967	2434
Missense in Polyphen		63	64.093	0.98295		814
Synonymous	1.47	55	70.7	0.778	0.00000360	703
Loss of Function	0.579	7	8.86	0.790	4.42e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000848	0.000847
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000229	0.000229
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative C to U editing enzyme whose physiological substrate is not yet known. {ECO:0000250}.
• Pathway: Metabolism of RNA;Formation of the Editosome;mRNA Editing: C to U Conversion;mRNA Editing (Consensus)

Recessive Scores

• pRec: 0.0897

Intolerance Scores

• loftool: 0.867
• rvis_EVS: 2.11
• rvis_percentile_EVS: 97.88

Haploinsufficiency Scores

• pHI: 0.0999
• hipred: N
• hipred_score: 0.123
• ghis: 0.384

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.503

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Apobec4

Gene ontology

• Biological process: mRNA processing
• Molecular function: hydrolase activity;metal ion binding