AFP alpha fetoprotein [Homo sapiens (human)] - Gene

Summary

Official Symbol: AFPprovided by HGNC
Official Full Name: alpha fetoproteinprovided by HGNC
Primary source: HGNC:HGNC:317
See related: Ensembl:ENSG00000081051 MIM:104150; AllianceGenome:HGNC:317
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: AFPD; FETA; HPAFP
Summary: This gene encodes alpha-fetoprotein, a major plasma protein produced by the yolk sac and the liver during fetal life. Alpha-fetoprotein expression in adults is often associated with hepatocarcinoma and with teratoma, and has prognostic value for managing advanced gastric cancer. However, hereditary persistance of alpha-fetoprotein may also be found in individuals with no obvious pathology. The protein is thought to be the fetal counterpart of serum albumin, and the alpha-fetoprotein and albumin genes are present in tandem in the same transcriptional orientation on chromosome 4. Alpha-fetoprotein is found in monomeric as well as dimeric and trimeric forms, and binds copper, nickel, fatty acids and bilirubin. The level of alpha-fetoprotein in amniotic fluid is used to measure renal loss of protein to screen for spina bifida and anencephaly. [provided by RefSeq, Oct 2019]
Expression: Biased expression in kidney (RPKM 1.8) and liver (RPKM 1.6) See more
Orthologs: mouse all
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Genomic context

Location:: 4q13.3

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (73436221..73456174)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (76779943..76799830)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (74301938..74321891)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Structural characteristics of alpha-fetoprotein, including N-glycosylation, metal ion and fatty acid binding sites.
Title: Structural characteristics of alpha-fetoprotein, including N-glycosylation, metal ion and fatty acid binding sites.
Alpha-fetoprotein: Past, present, and future.
Title: Alpha-fetoprotein: Past, present, and future.
Role of Alpha-Fetoprotein in the Pathogenesis of Cancer.
Title: Role of Alpha-Fetoprotein in the Pathogenesis of Cancer.
Combination of serum alpha-fetoprotein, PIVKA- and glypican-3 in diagnosis of hepatocellular carcinoma: a meta-analysis.
Title: Combination of serum alpha-fetoprotein, PIVKA-Ⅱ and glypican-3 in diagnosis of hepatocellular carcinoma: a meta-analysis.
Cellular gp96 upregulates AFP expression by blocking NR5A2 SUMOylation and ubiquitination in hepatocellular carcinoma.
Title: Cellular gp96 upregulates AFP expression by blocking NR5A2 SUMOylation and ubiquitination in hepatocellular carcinoma.
Maternal First-Trimester Alpha-Fetoprotein and Placenta-Mediated Pregnancy Complications.
Title: Maternal First-Trimester Alpha-Fetoprotein and Placenta-Mediated Pregnancy Complications.
AFP deletion leads to anti-tumorigenic but pro-metastatic roles in liver cancers with concomitant CTNNB1 mutations.
Title: AFP deletion leads to anti-tumorigenic but pro-metastatic roles in liver cancers with concomitant CTNNB1 mutations.
AUF1 promotes hepatocellular carcinoma progression and chemo-resistance by post-transcriptionally upregulating alpha-fetoprotein expression.
Title: AUF1 promotes hepatocellular carcinoma progression and chemo-resistance by post-transcriptionally upregulating alpha-fetoprotein expression.
Polyunsaturated Fatty Acid-Bound alpha-Fetoprotein Promotes Immune Suppression by Altering Human Dendritic Cell Metabolism.
Title: Polyunsaturated Fatty Acid-Bound α-Fetoprotein Promotes Immune Suppression by Altering Human Dendritic Cell Metabolism.
A Retrospective Multicentric Study of 34 Patients with Niemann-Pick Type C Disease and Early Liver Involvement in France.
Title: A Retrospective Multicentric Study of 34 Patients with Niemann-Pick Type C Disease and Early Liver Involvement in France.

Submit: New GeneRIF Correction See all GeneRIFs (346)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Alpha-fetoprotein deficiency MedGen: C1863081 OMIM: 615969 GeneReviews: Not available	not available
Alpha-fetoprotein, hereditary persistence of MedGen: C1863080 OMIM: 615970 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
A genome wide association study of genetic loci that influence tumour biomarkers cancer antigen 19-9, carcinoembryonic antigen and &#x000ce;&#x000b1; fetoprotein and their associations with cancer risk. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Human alpha-fetoprotein specifically interacts with HIV-1 gp120/gp41 (Env) and inhibits infection of primary macrophages by macrophage-tropic HIV-1 strains	PubMed
Envelope transmembrane glycoprotein gp41	env	Human alpha-fetoprotein specifically interacts with HIV-1 gp120/gp41 (Env) and inhibits infection of primary macrophages by macrophage-tropic HIV-1 strains	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-107546 (e-PCR)
- UniSTS:173842

SHGC-50928 (e-PCR)
- UniSTS:31278

D4S3144 (e-PCR)
- UniSTS:11591

MARC_3052-3053:991936680:1 (e-PCR)
- UniSTS:230984

SHGC-67270 (e-PCR)
- UniSTS:26749

MARC_15793-15794:1013620256:1 (e-PCR)
- UniSTS:267903

SHGC-59540 (e-PCR)
- UniSTS:77787

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in homeostasis of number of cells	IEA Inferred from Electronic Annotation more info
involved_in immune response	IEA Inferred from Electronic Annotation more info
involved_in ovulation from ovarian follicle	IEA Inferred from Electronic Annotation more info
involved_in progesterone metabolic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
located_in extracellular space	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: alpha-fetoprotein

Names: alpha-1-fetoprotein; alpha-fetoglobulin

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_023028.2 RefSeqGene

Range

5002..24955

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001134.3 → NP_001125.1 alpha-fetoprotein isoform 1 precursor

See identical proteins and their annotated locations for NP_001125.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC108157

Consensus CDS

CCDS3556.1

UniProtKB/Swiss-Prot

B2RBU3, P02771

UniProtKB/TrEMBL

J3KMX3

Related

ENSP00000379138.2, ENST00000395792.7

Conserved Domains (1) summary

smart00103
Location:404 → 594

ALBUMIN; serum albumin
NM_001354717.2 → NP_001341646.2 alpha-fetoprotein isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.

Source sequence(s)

AC108157

UniProtKB/TrEMBL

B4DMX4

Conserved Domains (2) summary

smart00103
Location:246 → 436

ALBUMIN; serum albumin

cl00031
Location:1 → 50

ALBUMIN; Albumin domain, contains five or six internal disulphide bonds; albuminoid superfamily includes alpha-fetoprotein which binds various cations, fatty acids and bilirubin; vitamin D-binding protein which binds to vitamin D, its metabolites, and fatty acids; ...