Gene Gene information from NCBI Gene database.
Entrez ID 9842
Gene name Pleckstrin homology and RUN domain containing M1
Gene symbol PLEKHM1
Synonyms (NCBI Gene)
AP162B2OPTA3OPTB6
Chromosome 17
Chromosome location 17q21.31
Summary 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.
3
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.
259
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 (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
26
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 identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
611466 29017 ENSG00000225190
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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
 
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
8
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Autosomal recessive osteopetrosis 6 Pathogenic rs786205055 RCV000000970
Osteopetrosis, autosomal dominant 3 Likely pathogenic; Pathogenic rs1304090710, rs559224144, rs1567759023 RCV003989397
RCV000678395
RCV000678396
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Autosomal recessive osteopetrosis 1 Uncertain significance rs2510737454 RCV003159267
Disorder of bone Benign rs73984399 RCV006269457
Associations from Text MiningDisease 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