AP1G2

protein-coding

adaptor related protein complex 1 subunit gamma 2, the group of Clathrin/coatomer adaptor, adaptin-like, N-terminal domain containing|Adaptor related protein complex 1

Gene summary

Adaptins are important components of clathrin-coated vesicles transporting ligand-receptor complexes from the plasma membrane or from the trans-Golgi network to lysosomes. The adaptin family of proteins is composed of four classes of molecules named alpha, beta-, beta prime- and gamma- adaptins. Adaptins, together with medium and small subunits, form a heterotetrameric complex called an adaptor, whose role is to promote the formation of clathrin-coated pits and vesicles. The protein encoded by this gene is a gamma-adaptin protein and it belongs to the adaptor complexes large subunits family. This protein along with the complex is thought to function at some trafficking step in the complex pathways between the trans-Golgi network and the cell surface. [provided by RefSeq, Aug 2017]

MANE transcript

NM_003917.5

Inheritance

—

ClinVar variants

P:1U:135B:8

Top phenotype

AP1G2-related disorder

gnomAD constraint

pLI —, LoF o/e 0.96

Max pathogenic AF

—

Genomic locus

chr14:23,559,565-23,568,070

External References & Databases

Ensembl (ENSG00000213983)

Transcript & Mutation Effects

hg38 • Region Span ~8.5 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 AP1G2 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 130

AP1G2-related disorderTotal: 1

Esophageal atresia/tracheoesophageal fistulaTotal: 1

Global developmental delayTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003917.5. 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			1 clinvar			1
missense		1 clinvar	129 clinvar	8 clinvar		138
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	1	135	8	0	144

Highest pathogenic variant AF is 0.00005391691

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 165 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003917.5	RefSeq	NP_003908.1	21	MANE Select
ENST00000397120.8	Ensembl	ENSP00000380309.3	21	MANE Select
NM_001282474.2	RefSeq	NP_001269403.1	11	Standard
NM_001282475.2	RefSeq	NP_001269404.1	18	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
ap1g2	Danio rerio	Structure: blood cell Quality: mislocalised abnormal

Gene / Model

Organism

Observed Phenotype

ap1g2

Danio rerio

Structure: blood cell

Quality: mislocalised

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Lysosome - Homo sapiens (human)
Lysosome Vesicle Biogenesis
Clathrin derived vesicle budding
trans-Golgi Network Vesicle Budding
Vesicle-mediated transport

Biological Process

intracellular protein transport
viral process
vesicle-mediated transport

Molecular Function

protein binding

Cellular Component

Golgi membrane
Golgi apparatus
Golgi-associated vesicle
endosome membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000308724
Coding exons: 21
Length: 8506
Individuals with no LoFs: 125090
Homozygous LoFs: 2
Heterozygous LoFs: 656
Defined: 125748
p: 0.00262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.391	449	473	0.949	0.0000273	5042
Missense (PolyPhen)		185	187.49	0.98669		2124
Synonymous	1.02	167	185	0.905	0.00000955	1691
Loss of Function	0.267	43	44.9	0.957	0.00000263	435

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0019	0.0019	notable
Latino/Admixed American	0.0028	0.0027	notable
Ashkenazi Jewish	0.0038	0.0038	notable
East Asian	0.0011	0.0011	notable
Finnish	0.0010	0.0010	notable
European (Non-Finnish)	0.0033	0.0033	notable
South Asian	0.0019	0.0018	notable
Other	0.0038	0.0038	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May function in protein sorting in late endosomes or multivesucular bodies (MVBs). {ECO:0000269|PubMed:9733768}.;

Recessive Scores

pRec: 0.0972

Intolerance Scores

LoFtool: 0.976
RVIS EVS: -1.24
RVIS percentile EVS: 5.52

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.911

Gene Damage Prediction

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