AP5B1

protein-coding

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

Gene summary

Involved in endosomal transport. Located in lysosomal membrane. Part of AP-type membrane coat adaptor complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_138368.5

Inheritance

—

ClinVar variants

P:7U:138B:13

Top phenotype

Macular dystrophy with variable extraocular manifestations

gnomAD constraint

pLI —, LoF o/e 0.84

Max pathogenic AF

—

Genomic locus

chr11:65,773,898-65,780,976

External References & Databases

Ensembl (ENSG00000254470)

Transcript & Mutation Effects

hg38 • Region Span ~7.1 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 AP5B1 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 145

not providedTotal: 5

Macular dystrophy with variable extraocular manifestationsTotal: 5

Hereditary spastic paraplegiaTotal: 3

Macular dystrophy with or without extraocular featuresTotal: 3

AP5B1-associated macular dystrophyTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138368.5. 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				4 clinvar		4
missense		2 clinvar	138 clinvar	9 clinvar		149
nonsense		2 clinvar				2
start loss						0
frameshift		3 clinvar				3
splice donor/acceptor (+/-2bp)						0
Total	0	7	138	13	0	158

Highest pathogenic variant AF is 0.000631166

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138368.5	RefSeq	NP_612377.4	2	MANE Select
ENST00000532090.3	Ensembl	ENSP00000454303.1	2	MANE Select
ENST00000893259.1	Ensembl	ENSP00000563318.1	2	Standard
ENST00000893259.2	Ensembl	ENSP00000563318.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein transport
endosomal transport

Molecular Function

protein binding

Cellular Component

lysosomal membrane
AP-type membrane coat adaptor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000532090
Coding exons: 2
Length: 4910
Individuals with no LoFs: 124489
Homozygous LoFs: 0
Heterozygous LoFs: 47
Defined: 124536
p: 0.000189

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.687	506	464	1.09	0.0000291	5317
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00047	0.00045	rare
Latino/Admixed American	0.00021	0.00020	rare
Ashkenazi Jewish	0.00021	0.00020	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00023	0.00023	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

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}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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