ARPIN-AP3S2

ARPIN-AP3S2 readthrough

Basic information

Region (hg38): 15:89834307-89912882

Previous symbols: [ "C15orf38-AP3S2" ]

Links

ENSG00000250021 ∙ NCBI:100526783 ∙ ∙ HGNC:38824 ∙ ∙ ∙ 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 ARPIN-AP3S2 gene.

• Inborn genetic diseases (15 variants)
• Seizure (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARPIN-AP3S2 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						0
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding			1			1
Total	0	0	16	0	0

Variants in ARPIN-AP3S2

This is a list of pathogenic ClinVar variants found in the ARPIN-AP3S2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-89835538-G-A		not specified	Uncertain significance (Sep 21, 2021)
15-89835627-G-A		not specified	Uncertain significance (Dec 28, 2023)
15-89837648-C-G		not specified	Uncertain significance (Apr 25, 2022)
15-89871516-C-T		not specified	Uncertain significance (Dec 14, 2023)
15-89888534-A-G		not specified	Uncertain significance (Jan 24, 2023)
15-89888588-G-A		not specified	Uncertain significance (Feb 22, 2023)
15-89893882-A-G		not specified	Uncertain significance (Jul 14, 2023)
15-89903224-C-T		not specified	Uncertain significance (Jun 04, 2024)
15-89903239-C-T		not specified	Uncertain significance (May 30, 2024)
15-89903255-C-A		not specified	Uncertain significance (Sep 20, 2023)
15-89903269-C-A		not specified	Uncertain significance (Dec 17, 2023)
15-89903325-T-C		not specified	Uncertain significance (Sep 06, 2022)
15-89903328-C-A		not specified	Uncertain significance (Apr 22, 2024)
15-89903335-A-G		not specified	Uncertain significance (Feb 03, 2022)
15-89903340-C-T		not specified	Uncertain significance (Sep 12, 2023)
15-89903379-T-C		not specified	Uncertain significance (Nov 14, 2023)
15-89903792-C-T		not specified	Uncertain significance (May 31, 2023)
15-89903809-C-T		not specified	Uncertain significance (Jul 08, 2022)
15-89903810-G-A		not specified	Uncertain significance (May 20, 2024)
15-89903869-G-A		not specified	Uncertain significance (Nov 09, 2023)
15-89903870-C-T		not specified	Uncertain significance (Jan 16, 2024)
15-89903917-G-A		not specified	Uncertain significance (Jan 09, 2024)
15-89903941-G-A		not specified	Uncertain significance (Feb 28, 2023)
15-89903945-C-T		not specified	Uncertain significance (May 31, 2023)
15-89903965-T-G		not specified	Uncertain significance (Dec 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARPIN-AP3S2	protein_coding	protein_coding	ENST00000398333	10	78575

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.15e-11	0.0906	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.153	231	238	0.972	0.0000143	2578
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00102	0.00101
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000229	0.000229
Middle Eastern	0.000110	0.000109
South Asian	0.000229	0.000229
Other	0.000657	0.000652

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.87
• rvis_percentile_EVS: 10.73

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N

Gene Damage Prediction

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

Gene ontology

• Biological process: intracellular protein transport;vesicle-mediated transport;negative regulation of actin nucleation
• Cellular component: membrane coat;intracellular membrane-bounded organelle