ARPIN-AP3S2

protein-coding

ARPIN-AP3S2 readthrough

Gene summary

This locus represents naturally occurring read-through transcription between the neighboring C15orf38 (chromosome 15 open reading frame 38) and AP3S2 (adaptor-related protein complex 3, sigma 2 subunit) genes. The read-through transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Nov 2010]

Previous symbols:

C15orf38-AP3S2

MANE transcript

N/A

Inheritance

—

ClinVar variants

U:15

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.9

Max pathogenic AF

—

Genomic locus

chr15:89,834,308-89,912,882

External References & Databases

Ensembl (ENSG00000250021)

NCBI Gene (100526783)

HGNC:38824

GenCC

ClinVar (ARPIN-AP3S2)

Transcript & Mutation Effects

hg38 • Region Span ~78.6 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 ARPIN-AP3S2 variants in ClinVar

2 Conditions Cataloged

Inborn genetic diseasesTotal: 15

SeizureTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . 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						0
missense			14 clinvar			14
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	15	0	0	15

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001199058.2	RefSeq	NP_001185987.1	10	Standard
ENST00000398333.7	Ensembl	ENSP00000381377.3	10	Standard
ENST00000558648.5	Ensembl	ENSP00000453100.1	5	Standard
ENST00000559629.1	Ensembl	ENSP00000453637.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

intracellular protein transport
vesicle-mediated transport
negative regulation of actin nucleation

Cellular Component

membrane coat
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000398333
Coding exons: 10
Length: 78575
Individuals with no LoFs: 125682
Homozygous LoFs: 0
Heterozygous LoFs: 66
Defined: 125748
p: 0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.153	231	238	0.972	0.0000143	2578
Missense (PolyPhen)		83	103.58	0.80133		1176
Synonymous	-0.479	105	98.9	1.06	0.00000637	764
Loss of Function	0.411	18	20.0	0.901	9.97e-7	236

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00044	0.00043	rare
Latino/Admixed American	0.00058	0.00058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00023	0.00023	rare
South Asian	0.00023	0.00023	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.87
RVIS percentile EVS: 10.73

Essentials

Essential (CRISPR): N

Gene Damage Prediction

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