AP5M1

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

Basic information

Region (hg38): 14:57268924-57298742

Previous symbols: [ "C14orf108", "MUDENG" ]

Links

ENSG00000053770 ∙ NCBI:55745 ∙ OMIM:614368 ∙ HGNC:20192 ∙ Uniprot:Q9H0R1 ∙ 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 AP5M1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AP5M1 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			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	0

Variants in AP5M1

This is a list of pathogenic ClinVar variants found in the AP5M1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-57269324-C-T		not specified	Uncertain significance (Aug 12, 2021)
14-57269327-G-A		not specified	Uncertain significance (Apr 01, 2024)
14-57269330-G-C		not specified	Uncertain significance (Sep 16, 2021)
14-57269344-C-A		not specified	Uncertain significance (Dec 19, 2023)
14-57274296-G-A		not specified	Uncertain significance (Feb 10, 2022)
14-57274396-C-T		not specified	Uncertain significance (Aug 02, 2021)
14-57274398-C-T		not specified	Uncertain significance (Dec 22, 2023)
14-57274399-G-A		not specified	Likely benign (Jul 19, 2023)
14-57274401-A-G		not specified	Uncertain significance (Aug 16, 2021)
14-57274462-C-G		not specified	Uncertain significance (Dec 07, 2022)
14-57274492-G-A		not specified	Uncertain significance (Jan 03, 2024)
14-57274519-C-T		not specified	Uncertain significance (May 23, 2024)
14-57274525-G-A		not specified	Uncertain significance (Nov 17, 2022)
14-57274542-G-A		not specified	Likely benign (Jul 06, 2022)
14-57274603-G-T		not specified	Uncertain significance (Sep 28, 2022)
14-57274632-A-G		not specified	Uncertain significance (Nov 19, 2022)
14-57274732-C-A		not specified	Uncertain significance (Jun 10, 2024)
14-57274749-A-C		not specified	Uncertain significance (Oct 13, 2023)
14-57274834-A-G		not specified	Uncertain significance (Sep 07, 2022)
14-57282126-A-C		not specified	Uncertain significance (Oct 29, 2021)
14-57282195-A-C		not specified	Uncertain significance (Mar 02, 2023)
14-57282205-A-T		not specified	Uncertain significance (Oct 13, 2023)
14-57282210-A-G		not specified	Uncertain significance (Jul 15, 2021)
14-57282993-A-G		not specified	Uncertain significance (Jun 16, 2024)
14-57286274-C-T		not specified	Uncertain significance (May 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AP5M1	protein_coding	protein_coding	ENST00000261558	8	21171

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.33e-9	0.570	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.127	245	251	0.977	0.0000120	3187
Missense in Polyphen		58	65.662	0.88331		853
Synonymous	-0.674	97	88.9	1.09	0.00000410	946
Loss of Function	1.22	17	23.4	0.727	0.00000125	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000304	0.000303
Ashkenazi Jewish	0.00	0.00
East Asian	0.000220	0.000217
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000179	0.000176
Middle Eastern	0.000220	0.000217
South Asian	0.000994	0.000980
Other	0.000326	0.000163

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:18395520, it may play a role in cell death. {ECO:0000269|PubMed:18395520, ECO:0000269|PubMed:22022230}.

Intolerance Scores

• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.55

Haploinsufficiency Scores

• pHI: 0.796
• hipred: Y
• hipred_score: 0.647
• ghis: 0.520

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: Ap5m1

Gene ontology

• Biological process: protein transport;endosomal transport
• Cellular component: lysosome;lysosomal membrane;late endosome;cytosol;membrane;AP-type membrane coat adaptor complex;late endosome membrane