SERPINA2 serpin family A member 2 (gene/pseudogene) [Homo sapiens (human)] - Gene

Summary

Official Symbol: SERPINA2provided by HGNC
Official Full Name: serpin family A member 2 (gene/pseudogene)provided by HGNC
Primary source: HGNC:HGNC:8985
See related: Ensembl:ENSG00000258597 MIM:107410; AllianceGenome:HGNC:8985
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: ATR; PIL; ARGS; psiATR; SERPINA2P
Summary: This gene encodes a member of the serpin family of proteins, a group of proteins that inhibit serine proteases. The encoded intracellular glycoprotein is localized at the endoplasmic reticulum. This gene is a polymorphic pseudogene, with the non-functional allele being predominant in some populations. Some individuals, as represented by the reference genome allele, contain a 2kb coding region deletion and a start code mutation. [provided by RefSeq, Feb 2014]
Annotation information: Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.; Note: Population studies indicate that this gene is polymorphic. Deletions, frameshift mutations and a critical start codon mutation (ATG->ATA) have been found in some populations as well as an allele that can encode a functional protein. This gene may be an evolving pseudogene (PMID: 17135331). The reference genome contains the start codon mutation and has a coding region deletion. The NCBI RefSeq Project therefore treats this as a pseudogene. [13 Feb 2013]
Expression: Low expression observed in reference dataset See more
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Genomic context

Location:: 14q32.13

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (94364318..94366702, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (88593837..88596220, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (94830655..94833039, complement)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: 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?

Specific features of SERPINA2 include the absence of insoluble aggregates and the insignificant response to cell stress, suggesting that it is a non-polymerogenic protein with divergent activity of SERPINA1.
Title: SERPINA2 is a novel gene with a divergent function from SERPINA1.
Observational study of gene-disease association. (HuGE Navigator)
Title: A linkage disequilibrium between genes at the serine protease inhibitor gene cluster on chromosome 14q32.1 is associated with Wegener's granulomatosis.
Clinical trial and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Molecular genetics of successful smoking cessation: convergent genome-wide association study results.
Study found that a common haplotype in Africa had a 2-kb deletion in the SERPINA2 gene is associated with remarkable long-range homozygozity as if it was quickly driven to high frequency by natural selection acting on an advantageous variant.
Title: Sequence diversity at the proximal 14q32.1 SERPIN subcluster: evidence for natural selection favoring the pseudogenization of SERPINA2.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

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 gp160, precursor	env	Alpha1-Antitrypsin (alpha(1)AT) is cleaved by serine proteases, causing a conformational change in alpha(1)AT that sequesters HIV-1 protease, blocks both HIV-1 gp160 and p55 processing, and is a powerful inhibitor of HIV replication	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

huma1ar2 (e-PCR)
- UniSTS:1627

D14S1142 (e-PCR)
- UniSTS:148587

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables serine-type endopeptidase inhibitor activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in negative regulation of endopeptidase activity	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: alpha-1-antitrypsin-related protein

Names: AAT-related protein; alpha-1 antitrypsin-related protein; putative alpha-1-antitrypsin-related protein; serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 2; serpin A2; serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 2, pseudogene

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.

mRNA and Protein(s)

NM_006220.3 → NP_006211.2 alpha-1-antitrypsin-related protein precursor

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the protein coding transcript. This allele is not found in the reference genome.

Source sequence(s)

AC235087

UniProtKB/Swiss-Prot

A0A0G2JPK4, P20848, S4UD68

Conserved Domains (1) summary

smart00093
Location:62 → 418

SERPIN; SERine Proteinase INhibitors

RNA

NR_110563.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2, non-coding) represents the non-protein coding transcript. The non-coding allele, found in the reference genome, contains a 2 kb deletion and a start codon mutation when compared to the protein coding allele.

Source sequence(s)

AL117259

Related

ENST00000553483.4

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000014.9 Reference GRCh38.p14 Primary Assembly

Range

94364318..94366702 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

NT_187601.1 Reference GRCh38.p14 ALT_REF_LOCI_1

Range

1478202..1488979 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060938.1 Alternate T2T-CHM13v2.0

Range

88593837..88596220 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NG_032041.1: Suppressed sequence

Description

NG_032041.1: This RefSeq was permanently suppressed because it is now thought that this gene does encode a protein.