AP1AR

adaptor related protein complex 1 associated regulatory protein

Basic information

Region (hg38): 4:112231740-112273110

Previous symbols: [ "C4orf16" ]

Links

ENSG00000138660 ∙ NCBI:55435 ∙ OMIM:610851 ∙ HGNC:28808 ∙ Uniprot:Q63HQ0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AP1AR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AP1AR 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			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	1

Variants in AP1AR

This is a list of pathogenic ClinVar variants found in the AP1AR region.

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

Position	Type	Phenotype	Significance	ClinVar
4-112232119-T-C		not specified	Uncertain significance (Feb 06, 2023)
4-112232120-T-G		not specified	Uncertain significance (Mar 02, 2023)
4-112232131-C-G		not specified	Uncertain significance (Mar 07, 2024)
4-112232144-G-A		not specified	Uncertain significance (Aug 30, 2022)
4-112232153-A-G		not specified	Uncertain significance (Nov 21, 2023)
4-112232171-G-C		not specified	Uncertain significance (Apr 22, 2024)
4-112253210-C-T		not specified	Uncertain significance (Mar 18, 2024)
4-112260815-T-C		not specified	Uncertain significance (Mar 16, 2022)
4-112260824-G-A		not specified	Uncertain significance (Nov 14, 2024)
4-112260837-A-G		not specified	Uncertain significance (Mar 17, 2023)
4-112260838-T-A		not specified	Uncertain significance (Aug 11, 2022)
4-112263025-A-C		not specified	Uncertain significance (Jun 02, 2023)
4-112263046-G-A		not specified	Uncertain significance (Feb 09, 2025)
4-112263073-G-A		not specified	Uncertain significance (Jan 16, 2024)
4-112263078-C-T		not specified	Uncertain significance (Sep 08, 2024)
4-112265786-T-C		not specified	Uncertain significance (Sep 04, 2024)
4-112265787-A-G		not specified	Uncertain significance (May 29, 2024)
4-112266648-C-T		not specified	Uncertain significance (Jan 19, 2025)
4-112266662-A-G		not specified	Uncertain significance (Dec 16, 2023)
4-112268216-A-T		not specified	Uncertain significance (Jul 25, 2024)
4-112268326-G-A		not specified	Uncertain significance (Jan 16, 2024)
4-112268352-A-G			Benign (Jun 08, 2018)
4-112268381-A-T		not specified	Uncertain significance (Jun 05, 2024)
4-112268389-A-G		not specified	Likely benign (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AP1AR	protein_coding	protein_coding	ENST00000274000	10	38311

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.142	0.857	125712	0	18	125730	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.19	103	143	0.719	0.00000718	1969
Missense in Polyphen		44	66.585	0.66081		969
Synonymous	0.184	48	49.7	0.967	0.00000260	521
Loss of Function	2.95	5	18.8	0.266	9.42e-7	253

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000296	0.0000296
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000186	0.000185
European (Non-Finnish)	0.0000631	0.0000615
Middle Eastern	0.000218	0.000217
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Necessary for adaptor protein complex 1 (AP-1)-dependent transport between the trans-Golgi network and endosomes. Regulates the membrane association of AP1G1/gamma1-adaptin, one of the subunits of the AP-1 adaptor complex. The direct interaction with AP1G1/gamma1-adaptin attenuates the release of the AP-1 complex from membranes. Regulates endosomal membrane traffic via association with AP-1 and KIF5B thus linking kinesin-based plus- end-directed microtubular transport to AP-1-dependent membrane traffic. May act as effector of AP-1 in calcium-induced endo- lysosome secretion. Inhibits Arp2/3 complex function; negatively regulates cell spreading, size and motility via intracellular sequestration of the Arp2/3 complex. {ECO:0000269|PubMed:15775984, ECO:0000269|PubMed:19706427, ECO:0000269|PubMed:21525240, ECO:0000269|PubMed:22689987}.

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.760
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.27

Haploinsufficiency Scores

• pHI: 0.148
• hipred: Y
• hipred_score: 0.685
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ap1ar

Gene ontology

• Biological process: negative regulation of receptor recycling;protein transport;regulation of Arp2/3 complex-mediated actin nucleation;cellular protein localization;vesicle targeting, trans-Golgi to endosome;negative regulation of substrate adhesion-dependent cell spreading;negative regulation of cell motility
• Cellular component: endosome;early endosome;late endosome;Golgi apparatus;cytosol;transport vesicle
• Molecular function: kinesin binding;AP-1 adaptor complex binding