AP1B1

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

Basic information

Region (hg38): 22:29327680-29388583

Previous symbols: [ "ADTB1", "CLAPB2" ]

Links

ENSG00000100280 ∙ NCBI:162 ∙ OMIM:600157 ∙ HGNC:554 ∙ Uniprot:Q10567 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ichthyosiform erythroderma, corneal involvement, and hearing loss (Strong), mode of inheritance: AR
• ichthyosiform erythroderma, corneal involvement, and hearing loss (Moderate), mode of inheritance: AR
• MEDNIK syndrome (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Keratitis-ichthyosis-deafness syndrome, autosomal recessive	AR	Audiologic/Otolaryngologic	The condition may include hearing loss, recognition and interventions related to speech and language development may be beneficial	Audiologic/Otolaryngologic; Dermatologic	31630788; 31630791

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AP1B1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AP1B1 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				5	3	8
missense			33	6		39
nonsense						0
start loss		1				1
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			2	3		5
non coding					21	21
Total	0	1	34	11	24

Variants in AP1B1

This is a list of pathogenic ClinVar variants found in the AP1B1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-29328675-G-A			Benign (May 20, 2021)
22-29328803-T-C			Benign (May 10, 2021)
22-29328814-C-T		AP1B1-related disorder	Likely benign (May 29, 2024)
22-29328856-C-T		Inborn genetic diseases	Uncertain significance (Mar 20, 2024)
22-29328892-A-T		Inborn genetic diseases	Uncertain significance (Sep 15, 2021)
22-29330406-C-T		AP1B1-related disorder • Inborn genetic diseases	Likely benign (Nov 15, 2023)
22-29330422-C-A		Inborn genetic diseases	Uncertain significance (Aug 28, 2023)
22-29330422-C-T		Inborn genetic diseases	Uncertain significance (Apr 27, 2024)
22-29330431-C-G		Inborn genetic diseases	Uncertain significance (Feb 27, 2024)
22-29330431-C-T		Inborn genetic diseases	Uncertain significance (Nov 09, 2021)
22-29330461-T-C		Inborn genetic diseases	Uncertain significance (Jun 17, 2024)
22-29330467-G-A		Autosomal recessive keratitis-ichthyosis-deafness syndrome	Pathogenic (Aug 08, 2022)
22-29330476-C-T		Inborn genetic diseases	Uncertain significance (Jan 30, 2024)
22-29330484-T-C		Inborn genetic diseases	Uncertain significance (Jun 02, 2023)
22-29330509-T-C		Inborn genetic diseases	Uncertain significance (Oct 29, 2021)
22-29330520-C-A		Inborn genetic diseases	Uncertain significance (Oct 03, 2022)
22-29330634-G-C		Inborn genetic diseases	Uncertain significance (May 31, 2023)
22-29331444-C-T		AP1B1-related disorder	Likely benign (Aug 02, 2023)
22-29331445-T-TCACC			Uncertain significance (Mar 01, 2022)
22-29331514-ATGT-A		Inborn genetic diseases	Uncertain significance (Feb 14, 2022)
22-29331852-C-A		Autosomal recessive keratitis-ichthyosis-deafness syndrome	Pathogenic (Jan 16, 2020)
22-29331877-C-T		Autosomal recessive keratitis-ichthyosis-deafness syndrome	Benign (Jul 14, 2021)
22-29331890-AG-A		Autosomal recessive keratitis-ichthyosis-deafness syndrome	Pathogenic (Aug 08, 2022)
22-29331891-G-C		Inborn genetic diseases	Uncertain significance (Mar 07, 2024)
22-29331915-A-G		Inborn genetic diseases	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AP1B1	protein_coding	protein_coding	ENST00000357586	22	95500

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00172	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.12	376	589	0.638	0.0000362	6188
Missense in Polyphen		81	173.78	0.4661		1851
Synonymous	-0.599	270	258	1.05	0.0000177	1909
Loss of Function	5.39	6	45.0	0.133	0.00000208	528

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000109
Finnish	0.000141	0.000139
European (Non-Finnish)	0.0000799	0.0000791
Middle Eastern	0.000112	0.000109
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

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;Fibroblast growth factor-1;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;FOXA1 transcription factor network;Validated nuclear estrogen receptor alpha network (Consensus)

Recessive Scores

• pRec: 0.225

Intolerance Scores

• loftool: 0.435
• rvis_EVS: -1.53
• rvis_percentile_EVS: 3.41

Haploinsufficiency Scores

• pHI: 0.550
• hipred: Y
• hipred_score: 0.736
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.799

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ap1b1
• Phenotype: growth/size/body region phenotype; cellular phenotype; immune system phenotype; skeleton phenotype; respiratory 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); hematopoietic system phenotype

Zebrafish Information Network

• Gene name: ap1b1
• Affected structure: neuromast hair cell
• Phenotype tag: abnormal
• Phenotype quality: functionality

Gene ontology

• Biological process: intracellular protein transport;determination of left/right symmetry;heart development;vesicle-mediated transport;antigen processing and presentation of exogenous peptide antigen via MHC class II;regulation of defense response to virus by virus
• Cellular component: Golgi membrane;lysosomal membrane;Golgi apparatus;cytosol;clathrin adaptor complex;cytoplasmic vesicle membrane;clathrin-coated vesicle membrane;trans-Golgi network membrane;intracellular membrane-bounded organelle
• Molecular function: transporter activity;protein binding;protein kinase binding;clathrin binding