AP5B1

adaptor related protein complex 5 subunit beta 1, the group of Armadillo like helical domain containing|Adaptor related protein complex 5

Basic information

Region (hg38): 11:65773897-65780976

Links

ENSG00000254470 ∙ NCBI:91056 ∙ OMIM:614367 ∙ HGNC:25104 ∙ Uniprot:Q2VPB7 ∙ 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 AP5B1 gene.

• Inborn genetic diseases (41 variants)
• not provided (4 variants)
• Hereditary spastic paraplegia (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AP5B1 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				4		4
missense			43	1		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	5	0

Variants in AP5B1

This is a list of pathogenic ClinVar variants found in the AP5B1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-65777893-G-A		not specified	Likely benign (Jan 26, 2022)
11-65777899-G-A		not specified	Uncertain significance (Dec 13, 2021)
11-65777906-C-T		not specified	Uncertain significance (Mar 16, 2022)
11-65777924-G-A		not specified	Uncertain significance (Jan 06, 2023)
11-65777986-G-A		not specified	Uncertain significance (Jun 02, 2023)
11-65777990-G-A		not specified	Uncertain significance (Feb 15, 2023)
11-65778103-C-T		not specified	Uncertain significance (Feb 28, 2023)
11-65778151-A-C		not specified	Uncertain significance (Sep 20, 2023)
11-65778301-C-T		not specified	Uncertain significance (Feb 06, 2023)
11-65778329-G-A		not specified	Uncertain significance (Feb 21, 2024)
11-65778368-C-G		not specified	Uncertain significance (Apr 19, 2023)
11-65778395-C-T		not specified	Uncertain significance (Apr 27, 2022)
11-65778404-A-G		Hereditary spastic paraplegia	Uncertain significance (Mar 07, 2017)
11-65778428-G-C		not specified	Uncertain significance (Apr 13, 2022)
11-65778500-G-A		not specified	Uncertain significance (Jan 23, 2023)
11-65778635-C-G		not specified	Uncertain significance (Jul 12, 2023)
11-65778655-C-T		not specified	Uncertain significance (Feb 06, 2023)
11-65778686-G-C		not specified	Uncertain significance (Sep 14, 2022)
11-65778702-C-G		Hereditary spastic paraplegia	Uncertain significance (Mar 07, 2017)
11-65778790-G-A		not specified	Uncertain significance (Apr 12, 2022)
11-65778804-C-T			Likely benign (Jun 05, 2018)
11-65778901-G-A		not specified	Uncertain significance (Apr 12, 2022)
11-65778940-G-A		not specified	Uncertain significance (Apr 19, 2023)
11-65778944-C-T		not specified	Uncertain significance (Jul 26, 2021)
11-65778957-G-C		not specified	Uncertain significance (Mar 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AP5B1	protein_coding	protein_coding	ENST00000532090	2	4910

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.27e-11	0.188	124489	0	47	124536	0.000189

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.687	506	464	1.09	0.0000291	5317
Missense in Polyphen		158	147.9	1.0683		1884
Synonymous	-2.34	268	224	1.20	0.0000132	2114
Loss of Function	0.709	18	21.6	0.835	0.00000115	234

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000672	0.000658
Ashkenazi Jewish	0.000209	0.000199
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000184	0.000177
Middle Eastern	0.000111	0.000111
South Asian	0.000232	0.000229
Other	0.000335	0.000331

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As part of AP-5, a probable fifth adaptor protein complex it may be involved in endosomal transport. {ECO:0000269|PubMed:22022230}.

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.170
• ghis: 0.539

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ap5b1

Gene ontology

• Biological process: protein transport;endosomal transport
• Cellular component: lysosomal membrane;AP-type membrane coat adaptor complex
• Molecular function: protein binding