ABCF1

protein-coding

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

Gene summary

The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the GCN20 subfamily. Unlike other members of the superfamily, this protein lacks the transmembrane domains which are characteristic of most ABC transporters. This protein may be regulated by tumor necrosis factor-alpha and play a role in enhancement of protein synthesis and the inflammation process. [provided by RefSeq, Jul 2008]

Previous symbols:

ABC50

MANE transcript

NM_001025091.2

Inheritance

—

ClinVar variants

U:99B:10

Top phenotype

Long QT syndrome

gnomAD constraint

pLI —, LoF o/e 0.44

Max pathogenic AF

—

Genomic locus

chr6:30,571,393-30,597,179

External References & Databases

Ensembl (ENSG00000204574)

Transcript & Mutation Effects

hg38 • Region Span ~25.8 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 ABCF1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 89

not providedTotal: 5

Long QT syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001025091.2. 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						0
missense			90 clinvar	8 clinvar	2 clinvar	100
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	99	8	2	109

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001025091.2	RefSeq	NP_001020262.1	25	MANE Select
ENST00000326195.13	Ensembl	ENSP00000313603.8	25	MANE Select
NM_001090.3	RefSeq	NP_001081.1	24	Standard
ENST00000376545.7	Ensembl	ENSP00000365728.3	24	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Transport of small molecules
ABC-family proteins mediated transport

Biological Process

translation
inflammatory response
transmembrane transport

Molecular Function

RNA binding
protein binding
ATP binding
translation factor activity, RNA binding
ATPase activity

Cellular Component

nuclear envelope
nucleoplasm
cytosol
ribosome
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000326195
Coding exons: 25
Length: 25804
Individuals with no LoFs: 125666
Homozygous LoFs: 0
Heterozygous LoFs: 82
Defined: 125748
p: 0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.51	330	486	0.679	0.0000287	5529
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00038	0.00037	rare
Latino/Admixed American	0.00058	0.00058	rare
Ashkenazi Jewish	0.00050	0.00050	rare
East Asian	0.00027	0.00027	rare
Finnish	0.00023	0.00018	rare
European (Non-Finnish)	0.00032	0.00029	rare
South Asian	0.00023	0.00023	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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}.;

Intolerance Scores

LoFtool: 0.321
RVIS EVS: -0.22
RVIS percentile EVS: 37.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.950

Gene Damage Prediction

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