ABCF1

ATP binding cassette subfamily F member 1, the group of ATP binding cassette subfamily F|MicroRNA protein coding host genes

Basic information

Region (hg38): 6:30571392-30597179

Previous symbols: [ "ABC50" ]

Links

ENSG00000204574 ∙ NCBI:23 ∙ OMIM:603429 ∙ HGNC:70 ∙ Uniprot:Q8NE71 ∙ 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 ABCF1 gene.

• Inborn genetic diseases (34 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCF1 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			32	2	2	36
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	2	2

Variants in ABCF1

This is a list of pathogenic ClinVar variants found in the ABCF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-30571492-C-G		not specified	Uncertain significance (Sep 16, 2021)
6-30577426-G-A		not specified	Uncertain significance (Jul 06, 2021)
6-30577441-A-C		not specified	Uncertain significance (Feb 27, 2023)
6-30577446-C-G		not specified	Uncertain significance (Mar 11, 2022)
6-30577854-G-A		not specified	Uncertain significance (Mar 24, 2023)
6-30577882-A-G		not specified	Uncertain significance (Sep 16, 2021)
6-30578092-A-G		not specified	Uncertain significance (Mar 29, 2023)
6-30578131-A-C		not specified	Uncertain significance (Jan 26, 2022)
6-30578133-G-A		not specified	Uncertain significance (Aug 10, 2021)
6-30578157-C-T		not specified	Uncertain significance (Nov 13, 2023)
6-30578353-G-A		not specified	Uncertain significance (Oct 04, 2022)
6-30578366-G-A		not specified	Uncertain significance (May 03, 2023)
6-30578507-G-A		not specified	Uncertain significance (Dec 03, 2021)
6-30580454-G-A		not specified	Uncertain significance (Jul 06, 2021)
6-30580502-G-A		not specified	Uncertain significance (Aug 30, 2021)
6-30580518-A-G		not specified	Uncertain significance (Dec 26, 2023)
6-30582398-C-T		not specified	Uncertain significance (Sep 16, 2021)
6-30582472-C-T		not specified	Uncertain significance (May 03, 2023)
6-30583100-C-T		not specified	Uncertain significance (Mar 11, 2024)
6-30583106-A-G		not specified	Likely benign (Feb 06, 2023)
6-30583146-G-A		not specified	Uncertain significance (May 04, 2022)
6-30583675-C-A		not specified	Uncertain significance (Jun 21, 2021)
6-30583806-A-C		not specified	Uncertain significance (Jun 29, 2023)
6-30583818-A-G		not specified	Uncertain significance (Jan 04, 2024)
6-30584276-G-A			Benign (Jul 26, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCF1	protein_coding	protein_coding	ENST00000326195	25	25804

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.28e-9	1.00	125666	0	82	125748	0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.51	330	486	0.679	0.0000287	5529
Missense in Polyphen		80	183.54	0.43586		1972
Synonymous	1.20	163	184	0.887	0.00000997	1565
Loss of Function	3.93	25	57.0	0.438	0.00000316	642

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000961	0.000950
Ashkenazi Jewish	0.000499	0.000496
East Asian	0.000274	0.000272
Finnish	0.000231	0.000185
European (Non-Finnish)	0.000315	0.000290
Middle Eastern	0.000274	0.000272
South Asian	0.000230	0.000229
Other	0.000332	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 2 is required for efficient Cap- and IRES- mediated mRNA translation initiation. Isoform 2 is not involved in the ribosome biogenesis. {ECO:0000269|PubMed:19570978}.
• Pathway: Transport of small molecules;ABC-family proteins mediated transport (Consensus)

Intolerance Scores

• loftool: 0.321
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.54

Haploinsufficiency Scores

• pHI: 0.153
• hipred: Y
• hipred_score: 0.627
• ghis: 0.537

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.950

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abcf1
• 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)

Gene ontology

• Biological process: translation;inflammatory response;transmembrane transport
• Cellular component: nuclear envelope;nucleoplasm;cytosol;ribosome;membrane
• Molecular function: RNA binding;protein binding;ATP binding;translation factor activity, RNA binding;ATPase activity