ABCF3

protein-coding

ATP binding cassette subfamily F member 3, the group of ATP binding cassette subfamily F

Gene summary

This gene encodes a member of the ATP-binding cassette (ABC) transporter superfamily. ATP-binding cassette proteins transport various molecules across extra- and intracellular membranes. The protein encoded by this gene displays antiviral effect against flaviviruses. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2017]

MANE transcript

NM_018358.3

Inheritance

—

ClinVar variants

U:118B:2

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr3:184,186,095-184,194,012

External References & Databases

Ensembl (ENSG00000161204)

Transcript & Mutation Effects

hg38 • Region Span ~7.9 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 ABCF3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 92

not providedTotal: 1

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018358.3. 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			4 clinvar	1 clinvar		5
missense			98 clinvar	1 clinvar		99
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			16 clinvar			16
Total	0	0	118	2	0	120

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 54 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018358.3	RefSeq	NP_060828.2	21	MANE Select
ENST00000429586.7	Ensembl	ENSP00000411471.2	21	MANE Select
NM_001351298.2	RefSeq	NP_001338227.1	21	Standard
NM_001351299.2	RefSeq	NP_001338228.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

defense response to virus

Molecular Function

protein binding
ATP binding
ATPase activity
cadherin binding

Cellular Component

membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000429586
Coding exons: 21
Length: 7990
Individuals with no LoFs: 125716
Homozygous LoFs: 0
Heterozygous LoFs: 32
Defined: 125748
p: 0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.654	392	430	0.911	0.0000273	4586
Missense (PolyPhen)		124	167.32	0.74111		1865
Synonymous	-0.00696	170	170	1.00	0.0000101	1415
Loss of Function	3.76	16	42.4	0.377	0.00000214	472

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00021	0.00021	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Displays an antiviral effect against flaviviruses such as west Nile virus (WNV) in the presence of OAS1B. {ECO:0000250}.;

Recessive Scores

pRec: 0.155

Intolerance Scores

LoFtool: 0.0790
RVIS EVS: -0.77
RVIS percentile EVS: 13.15

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.893

Gene Damage Prediction

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