Gene
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
9842
Gene name Gene Name - the full gene name approved by the HGNC.
Pleckstrin homology and RUN domain containing M1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
PLEKHM1
Synonyms (NCBI Gene) Gene synonyms aliases
AP162, B2, OPTA3, OPTB6
Chromosome Chromosome number
17
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
17q21.31
Summary Summary of gene provided in NCBI Entrez Gene.
The protein encoded by this gene is essential for bone resorption, and may play a critical role in vesicular transport in the osteoclast. Mutations in this gene are associated with autosomal recessive osteopetrosis type 6 (OPTB6). Alternatively spliced tr
SNPs SNP information provided by dbSNP.
SNP ID Visualize variation Clinical significance Consequence
rs559224144 G>A Pathogenic Non coding transcript variant, missense variant, coding sequence variant
rs786205055 C>G,T Pathogenic Genic upstream transcript variant, intron variant, splice donor variant, 5 prime UTR variant
rs1567759023 TG>- Pathogenic Frameshift variant, non coding transcript variant, genic downstream transcript variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
miRTarBase ID miRNA Experiments Reference
MIRT051055 hsa-miR-17-5p CLASH 23622248
MIRT047158 hsa-miR-183-5p CLASH 23622248
MIRT044379 hsa-miR-106b-5p CLASH 23622248
MIRT052883 hsa-miR-3909 CLASH 23622248
MIRT044379 hsa-miR-106b-5p PAR-CLIP 26701625
Gene ontology (GO) Gene ontology information of associated ontologies with gene provided by GO database.
GO ID Ontology Definition Evidence Reference
GO:0005515 Function Protein binding IPI 25500191, 27291868, 28325809, 33452816
GO:0005654 Component Nucleoplasm IDA
GO:0005730 Component Nucleolus IDA
GO:0005764 Component Lysosome IDA 28325809
GO:0005764 Component Lysosome IEA
Other IDs Other ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
MIM HGNC e!Ensembl
611466 29017 ENSG00000225190
Protein
UniProt ID Q9Y4G2
Protein name Pleckstrin homology domain-containing family M member 1 (PH domain-containing family M member 1) (162 kDa adapter protein) (AP162)
Protein function Acts as a multivalent adapter protein that regulates Rab7-dependent and HOPS complex-dependent fusion events in the endolysosomal system and couples autophagic and the endocytic trafficking pathways. Acts as a dual effector of RAB7A and ARL8B th
PDB 5DPR , 5DPS , 5DPT , 5DPW , 8JC5
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF02759 RUN 49 182 RUN domain Family
PF13901 zf-RING_9 846 1048 Putative zinc-RING and/or ribbon Domain
Tissue specificity TISSUE SPECIFICITY: Expressed in placenta, liver, prostate, thymus, spleen, ovary, colon, colon carcinoma and peripheral blood lymphocytes (PBL). Weakly expressed in brain, lung, kidney, and testis. No expression in heart, skeletal muscle, pancreas and sm
Sequence
MLSVVENGLDPQAAIPVIKKKLVGSVKALQKQYVSLDTVVTSEDGDANTMCSALEAVFIH
GLHAKHIRAEAGGKRKKSAHQKPLPQPVFWPLLKAVTHKHIISELEHLTFVNTDVGRCRA
WLRLALNDGLMECYLKLLLQEQARLHEYYQPTALLRDAEEGEFLLSFLQGLTSLSFELSY
KS
AILNEWTLTPLALSGLCPLSELDPLSTSGAELQRKESLDSISHSSGSEDIEVHHSGHK
IRRNQKLTASSLSLDTASSSQLSCSLNSDSCLLQENGSKSPDHCEEPMSCDSDLGTANAE
DSDRSLQEVLLEFSKAQVNSVPTNGLSQETEIPTPQASLSLHGLNTSTYLHCEAPAEPLP
AQAASGTQDGVHVQEPRPQAPSPLDLQQPVESTSGQQPSSTVSETAREVGQGNGLQKAQA
HDGAGLKLVVSSPTSPKNKSWISEDDFYRPSREQPLESASDHPIASYRGTPGSRPGLHRH
FSQEPRKNCSLGALDQACVPSPGRRQAQAAPSQGHKSFRVVHRRQMGLSNPFRGLMKLGT
VERRGAMGIWKELFCELSPLEFRLYLSNEEHTCVENCSLLRCESVGPAHSDGRFELVFSG
KKLALRASSQDEAEDWLDRVREALQKVRPQQEDEWVNVQYPDQPEEPPEAPQGCLSPSDL
LSEPAALQGTQFDWSSAQVPEPDAIKESLLYLYMDRTWMPYIFSLSLEALKCFRIRNNEK
MLSDSHGVETIRDILPDTSLGGPSFFKIITAKAVLKLQAGNAEEAALWRDLVRKVLASYL
ETAEEAVTLGGSLDENCQEVLKFATRENGFLLQYLVAIPMEKGLDSQGCFCAGCSRQIGF
SFVRPKLCAFSGLYYCDICHQDDASVIPARIIHNWDLTKRPICRQALKFLTQIRAQPLIN
LQMVNASLYEHVERMHLIGRRREQLKLLGDYLGLCRSGALKELSKRLNHRNYLLESPHRF
SVADLQQIADGVYEGFLKALIEFASQHVYHCDLCTQRGFICQICQHHDIIFPFEFDTTVR
CAECKTVFHQSCQAVVKKGCPRCARRRK
YQEQNIFA
Sequence length 1056
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  
  Autophagy - animal
Salmonella infection
 
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Associated diseases Disease associations categorized as Causal (pathogenic variants), Unknown (uncertain genetic evidence), or Text Mining (literature-based associations)
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Disease merge term Disease name dbSNP ID References
Osteopetrosis Autosomal recessive osteopetrosis 6, osteopetrosis, autosomal dominant 3 rs786205055, rs559224144, rs1567759023 N/A
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Disease merge term Disease name Evidence References Source
Neuroticism Neuroticism N/A N/A GWAS
Ovarian cancer Epithelial ovarian cancer N/A N/A GWAS
Associations from Text Mining Disease associations identified through Pubtator
Disease Name Relationship Type References
Bone Diseases Metabolic Associate 17997709
Carcinoma Basal Cell Associate 1375618
Carcinoma Ovarian Epithelial Associate 23535648
Dykes Markes Harper syndrome Associate 27291868
Neoplasms Associate 30982432
Osteopetrosis Associate 17997709, 20943950, 27291868, 32415263
Osteopetrosis mild autosomal recessive form Associate 17997709, 28816234
Osteosclerosis Associate 17997709
Ovarian Neoplasms Associate 23544013
Pancytopenia Associate 27291868