AP5S1

adaptor related protein complex 5 subunit sigma 1, the group of Adaptor related protein complex 5

Basic information

Region (hg38): 20:3811384-3828838

Previous symbols: [ "C20orf29" ]

Links

ENSG00000125843 ∙ NCBI:55317 ∙ OMIM:614824 ∙ HGNC:15875 ∙ Uniprot:Q9NUS5 ∙ 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 AP5S1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AP5S1 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				1		1
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	0

Variants in AP5S1

This is a list of pathogenic ClinVar variants found in the AP5S1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-3822121-G-A		not specified	Uncertain significance (May 23, 2023)
20-3822163-G-A		not specified	Uncertain significance (Aug 04, 2023)
20-3822179-G-A		not specified	Uncertain significance (Jul 14, 2022)
20-3822194-C-A		not specified	Uncertain significance (Jun 18, 2021)
20-3822265-C-T		not specified	Uncertain significance (Aug 02, 2021)
20-3823884-A-G		not specified	Uncertain significance (Apr 17, 2024)
20-3823890-C-T		not specified	Uncertain significance (May 16, 2024)
20-3823915-G-A		not specified	Uncertain significance (Dec 20, 2023)
20-3823923-A-G		not specified	Uncertain significance (Aug 14, 2023)
20-3823925-G-A		not specified	Uncertain significance (Sep 17, 2021)
20-3823925-G-T		not specified	Uncertain significance (Feb 28, 2023)
20-3823935-C-T		not specified	Uncertain significance (Nov 03, 2022)
20-3823937-G-A		not specified	Likely benign (Mar 01, 2024)
20-3823960-C-T		not specified	Uncertain significance (Feb 27, 2023)
20-3823977-C-T		not specified	Uncertain significance (Dec 11, 2023)
20-3824067-G-A		not specified	Uncertain significance (Nov 30, 2022)
20-3824077-C-G		not specified	Uncertain significance (Dec 17, 2021)
20-3824079-C-G		not specified	Uncertain significance (Nov 29, 2023)
20-3824116-T-G		not specified	Uncertain significance (Sep 06, 2022)
20-3824145-C-T		not specified	Uncertain significance (Dec 13, 2022)
20-3824155-C-T		not specified	Uncertain significance (May 23, 2023)
20-3824196-G-A		not specified	Uncertain significance (Nov 21, 2023)
20-3824217-C-T		not specified	Uncertain significance (Mar 15, 2024)
20-3824277-A-G		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AP5S1	protein_coding	protein_coding	ENST00000246041	2	4772

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000903	0.350	125721	0	23	125744	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.615	157	137	1.15	0.00000967	1257
Missense in Polyphen		41	36.025	1.1381		400
Synonymous	0.0427	61	61.4	0.993	0.00000404	460
Loss of Function	-0.0318	6	5.92	1.01	3.39e-7	56

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000324	0.000322
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000706	0.0000462
European (Non-Finnish)	0.0000887	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As part of AP-5, a probable fifth adaptor protein complex it may be involved in endosomal transport. According to PubMed:20613862, it is required for efficient homologous recombination DNA double-strand break repair. {ECO:0000269|PubMed:20613862, ECO:0000269|PubMed:22022230}.

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.0796
• hipred: N
• hipred_score: 0.341
• ghis: 0.514

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ap5s1

Gene ontology

• Biological process: double-strand break repair via homologous recombination;protein transport;endosomal transport
• Cellular component: nucleoplasm;lysosome;lysosomal membrane;late endosome;cytosol;AP-type membrane coat adaptor complex;late endosome membrane
• Molecular function: protein binding