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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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					4	4
missense			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			1			1
Total	0	0	22	1	4

Variants in A1CF

This is a list of pathogenic ClinVar variants found in the A1CF region.

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

Position	Type	Phenotype	Significance	ClinVar
10-50806818-G-T		not specified	Uncertain significance (Feb 15, 2023)
10-50806872-C-G		not specified	Uncertain significance (Mar 22, 2022)
10-50809929-A-G		not specified	Uncertain significance (May 15, 2024)
10-50810003-A-C		not specified	Uncertain significance (Jul 05, 2022)
10-50810014-C-A		not specified	Uncertain significance (May 11, 2022)
10-50810040-T-G		not specified	Uncertain significance (Aug 10, 2021)
10-50811112-A-G		not specified	Uncertain significance (May 16, 2024)
10-50813874-T-C		not specified	Uncertain significance (Nov 08, 2022)
10-50813904-T-C		not specified	Uncertain significance (Apr 25, 2022)
10-50813909-G-A		not specified	Uncertain significance (Jul 25, 2023)
10-50813909-G-C		not specified	Uncertain significance (Jan 16, 2024)
10-50814009-G-A		not specified	Uncertain significance (Sep 26, 2023)
10-50814012-C-T			Likely benign (Jun 23, 2018)
10-50814032-G-A		not specified	Uncertain significance (Dec 13, 2023)
10-50814037-C-T			Likely benign (Jun 23, 2018)
10-50816035-C-G		not specified	Uncertain significance (Oct 12, 2021)
10-50816265-G-A			Benign (Mar 05, 2018)
10-50820562-A-G		not specified	Uncertain significance (Oct 26, 2022)
10-50836093-C-T			Benign (Jul 31, 2018)
10-50836096-C-T		not specified	Uncertain significance (Dec 06, 2023)
10-50836203-C-A		not specified	Uncertain significance (Jan 03, 2022)
10-50841950-C-T		not specified	Uncertain significance (Feb 06, 2024)
10-50843994-A-G			Benign (Jun 14, 2018)
10-50844004-A-G		not specified	Uncertain significance (Dec 19, 2023)
10-50844014-C-T		not specified	Uncertain significance (Sep 06, 2022)

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
5.92e-10	0.959	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

Haploinsufficiency Scores

• pHI: 0.189
• hipred: Y
• hipred_score: 0.655
• ghis: 0.395

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

Mouse Genome Informatics

• Gene name: A1cf
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype

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