A1CF

APOBEC1 complementation factor, the group of RNA binding motif containing

Basic information

Region (hg38): 10:50799409-50885675

Links

ENSG00000148584 ∙ NCBI:29974 ∙ OMIM:618199 ∙ HGNC:24086 ∙ Uniprot:Q9NQ94 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 84.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_014576.4	NP_055391.2	11	yes	-
ENST00000373997.8	ENSP00000363109.3	11	yes	-
NM_138932.3	NP_620310.1	11	-	-
NM_138933.3	NP_620311.1	11	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the A1CF gene.

• not_specified (54 variants)
• not_provided (6 variants)
• Hereditary_breast_ovarian_cancer_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the A1CF gene is commonly pathogenic or not. These statistics are base on transcript: NM_014576.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	1	4	6
missense			56	1		57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	58	2	4

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
A1CF	protein_coding	protein_coding	ENST00000373995	11	86267

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125698	0	48	125746	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.990	274	324	0.845	0.0000159	3829
Missense in Polyphen		100	138.39	0.72259		1659
Synonymous	-0.306	125	121	1.04	0.00000633	1183
Loss of Function	2.10	20	33.0	0.605	0.00000211	362

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000276	0.000273
Middle Eastern	0.000164	0.000163
South Asian	0.000271	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the postranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. Binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. The complex also protects the edited APOB mRNA from nonsense-mediated decay. {ECO:0000269|PubMed:10669759, ECO:0000269|PubMed:10781591, ECO:0000269|PubMed:12881431}.
• Pathway: Metabolism of RNA;Formation of the Editosome;mRNA Editing: C to U Conversion;mRNA Editing (Consensus)

Recessive Scores

• pRec: 0.360

Intolerance Scores

• loftool: 0.877
• rvis_EVS: -0.38
• rvis_percentile_EVS: 28.01

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.542

Gene Damage Prediction

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

Gene ontology

• Biological process: mRNA processing;mRNA localization resulting in posttranscriptional regulation of gene expression;cytidine to uridine editing;mRNA modification;protein stabilization
• Cellular component: nucleus;nucleoplasm;cytoplasm;endoplasmic reticulum;apolipoprotein B mRNA editing enzyme complex
• Molecular function: RNA binding;double-stranded RNA binding;single-stranded RNA binding;mRNA binding;protein binding