AP1G1

adaptor related protein complex 1 subunit gamma 1, the group of Clathrin/coatomer adaptor, adaptin-like, N-terminal domain containing|Adaptor related protein complex 1|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 16:71729000-71809201

Previous symbols: [ "CLAPG1", "ADTG" ]

Links

ENSG00000166747 ∙ NCBI:164 ∙ OMIM:603533 ∙ HGNC:555 ∙ Uniprot:O43747 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Usmani-Riazuddin syndrome, autosomal dominant (Strong), mode of inheritance: AD
• Usmani-Riazuddin syndrome, autosomal recessive (Strong), mode of inheritance: AR
• complex neurodevelopmental disorder (Strong), mode of inheritance: AD
• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Usmani-Riazuddin syndrome, autosomal dominant	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	34102099

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AP1G1 gene.

• Usmani-Riazuddin syndrome, autosomal dominant (2 variants)
• Usmani-Riazuddin syndrome, autosomal recessive (1 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AP1G1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense		1	25	15		41
nonsense	2					2
start loss						0
frameshift		1	1			2
inframe indel		1				1
splice donor/acceptor (+/-2bp)	1	2	1			4
splice region				2		2
non coding				1	1	2
Total	3	5	27	17	1

Variants in AP1G1

This is a list of pathogenic ClinVar variants found in the AP1G1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-71734597-T-C			Benign (Mar 13, 2022)
16-71734629-T-C		AP1G1-related disorder	Uncertain significance (Dec 21, 2022)
16-71734632-T-C			Uncertain significance (Jun 14, 2024)
16-71734650-C-T			Uncertain significance (Mar 15, 2022)
16-71734652-G-A		not specified	Uncertain significance (Apr 23, 2024)
16-71738979-T-C			Uncertain significance (Aug 24, 2022)
16-71739083-T-C		AP1G1-related disorder	Likely benign (May 18, 2024)
16-71739261-G-A		Inborn genetic diseases	Pathogenic (Mar 04, 2022)
16-71739280-C-G		Inborn genetic diseases	Uncertain significance (Apr 12, 2023)
16-71739291-G-A		Inborn genetic diseases	Likely benign (Dec 05, 2022)
16-71739297-A-C		Inborn genetic diseases	Likely benign (Apr 18, 2023)
16-71739301-CT-C		Usmani-Riazuddin syndrome, autosomal dominant	Likely pathogenic (Feb 27, 2024)
16-71739315-C-T		Inborn genetic diseases	Uncertain significance (Mar 10, 2022)
16-71739316-AG-A			Uncertain significance (Feb 01, 2022)
16-71739333-C-T			Uncertain significance (Jun 07, 2024)
16-71745141-C-CA		AP1G1-related disorder	Uncertain significance (Jun 07, 2023)
16-71745159-C-T		Inborn genetic diseases	Likely benign (Dec 14, 2023)
16-71745197-G-A			Likely benign (Dec 01, 2023)
16-71745529-C-T		not specified	Uncertain significance (Jan 25, 2024)
16-71745549-A-G		Inborn genetic diseases	Likely benign (Sep 22, 2023)
16-71745558-G-A		Inborn genetic diseases	Likely benign (Feb 05, 2024)
16-71745558-G-C		Inborn genetic diseases	Uncertain significance (Aug 04, 2021)
16-71745559-T-C		Inborn genetic diseases	Likely benign (Mar 07, 2023)
16-71745596-TCTCTCAAGTAGGGC-GGG			Likely pathogenic (Jan 01, 2022)
16-71745612-G-C			Uncertain significance (Jul 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AP1G1	protein_coding	protein_coding	ENST00000393512	23	80192

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000230	125742	0	5	125747	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.98	277	456	0.607	0.0000242	5382
Missense in Polyphen		47	158.58	0.29637		1872
Synonymous	-0.303	165	160	1.03	0.00000796	1605
Loss of Function	6.05	5	52.2	0.0959	0.00000333	569

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000627	0.0000627
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000474	0.0000462
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Subunit of clathrin-associated adaptor protein complex 1 that plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The AP complexes mediate both the recruitment of clathrin to membranes and the recognition of sorting signals within the cytosolic tails of transmembrane cargo molecules.
• Pathway: Lysosome - Homo sapiens (human);Golgi Associated Vesicle Biogenesis;Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;Disease;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking;Host Interactions of HIV factors;HIV Infection;MHC class II antigen presentation;Infectious disease;Immune System;Adaptive Immune System;Nef mediated downregulation of MHC class I complex cell surface expression;Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters;The role of Nef in HIV-1 replication and disease pathogenesis (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.247
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.45

Haploinsufficiency Scores

• pHI: 0.473
• hipred: Y
• hipred_score: 0.783
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.961

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ap1g1
• Phenotype: hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: ap1g1
• Affected structure: blood cell
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: intracellular protein transport;antigen processing and presentation of exogenous peptide antigen via MHC class II;melanosome organization;endosome to melanosome transport;positive regulation of natural killer cell degranulation;positive regulation of natural killer cell mediated cytotoxicity;regulation of defense response to virus by virus;Golgi to lysosome transport
• Cellular component: Golgi membrane;cytoplasm;lysosomal membrane;Golgi apparatus;cytosol;membrane;AP-type membrane coat adaptor complex;AP-1 adaptor complex;clathrin-coated vesicle;cytoplasmic vesicle membrane;clathrin-coated vesicle membrane;trans-Golgi network membrane;intracellular membrane-bounded organelle;recycling endosome
• Molecular function: transporter activity;protein binding;Rab GTPase binding;kinesin binding;GTP-dependent protein binding