APOBEC4

protein-coding

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

Gene summary

This gene encodes a member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases, which convert cytidine to uridine. Other AID/APOBEC family members are involved in mRNA editing, somatic hypermutation and recombination of immunoglobulin genes, and innate immunity to retroviral infection. [provided by RefSeq, Jul 2008]

Previous symbols:

C1orf169

MANE transcript

NM_203454.3

Inheritance

—

ClinVar variants

U:45B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.79

Max pathogenic AF

—

Genomic locus

chr1:183,646,275-183,653,316

External References & Databases

Ensembl (ENSG00000173627)

Transcript & Mutation Effects

hg38 • Region Span ~7.0 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 APOBEC4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 48

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_203454.3. 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 clinvar	2
missense			44 clinvar	4 clinvar	3 clinvar	51
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	45	4	4	53

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_203454.3	RefSeq	NP_982279.1	1	MANE Select
ENST00000308641.6	Ensembl	ENSP00000310622.4	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of RNA
Formation of the Editosome
mRNA Editing: C to U Conversion
mRNA Editing

Biological Process

mRNA processing

Molecular Function

hydrolase activity
metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000308641
Coding exons: 1
Length: 6911
Individuals with no LoFs: 125697
Homozygous LoFs: 0
Heterozygous LoFs: 50
Defined: 125747
p: 0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.557	173	195	0.888	0.00000967	2434
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00023	0.00023	rare
South Asian	0.00013	0.00013	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Putative C to U editing enzyme whose physiological substrate is not yet known. {ECO:0000250}.;

Recessive Scores

pRec: 0.0897

Intolerance Scores

LoFtool: 0.867
RVIS EVS: 2.11
RVIS percentile EVS: 97.88

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.503

Gene Damage Prediction

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