Seroatlas · Human Serome Atlas

PDCD6IP

Programmed cell death 6-interacting protein

Also known as: AIP1, Alix, Hp95, PDC6I_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q8WUM4
Gene: PDCD6IP
Ensembl: ENSG00000170248
Chromosome: 3
Canonical length: 868 aa
Protein class: Human disease related genes, Plasma proteins, Predicted intracellular proteins
Subcellular location: Vesicles,Centrosome
Secretome location: Intracellular and membrane
Quaternary structure: Homooligomer

OverviewNCBI Gene

This gene encodes a protein that functions within the ESCRT pathway in the abscission stage of cytokinesis, in intralumenal endosomal vesicle formation, and in enveloped virus budding. Studies using mouse cells have shown that overexpression of this protein can block apoptosis. In addition, the product of this gene binds to the product of the PDCD6 gene, a protein required for apoptosis, in a calcium-dependent manner. This gene product also binds to endophilins, proteins that regulate membrane shape during endocytosis. Overexpression of this gene product and endophilins results in cytoplasmic vacuolization, which may be partly responsible for the protection against cell death. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. Related pseudogenes have been identified on chromosome 15. [provided by RefSeq, Jan 2012]

Canonical amino-acid sequenceUniProt

868 residues, UniProt reviewed canonical sequence.

>Q8WUM4|PDCD6IP
     1  MATFISVQLK KTSEVDLAKP LVKFIQQTYP SGGEEQAQYC RAAEELSKLR RAAVGRPLDK
    61  HEGALETLLR YYDQICSIEP KFPFSENQIC LTFTWKDAFD KGSLFGGSVK LALASLGYEK
   121  SCVLFNCAAL ASQIAAEQNL DNDEGLKIAA KHYQFASGAF LHIKETVLSA LSREPTVDIS
   181  PDTVGTLSLI MLAQAQEVFF LKATRDKMKD AIIAKLANQA ADYFGDAFKQ CQYKDTLPKE
   241  VFPVLAAKHC IMQANAEYHQ SILAKQQKKF GEEIARLQHA AELIKTVASR YDEYVNVKDF
   301  SDKINRALAA AKKDNDFIYH DRVPDLKDLD PIGKATLVKS TPVNVPISQK FTDLFEKMVP
   361  VSVQQSLAAY NQRKADLVNR SIAQMREATT LANGVLASLN LPAAIEDVSG DTVPQSILTK
   421  SRSVIEQGGI QTVDQLIKEL PELLQRNREI LDESLRLLDE EEATDNDLRA KFKERWQRTP
   481  SNELYKPLRA EGTNFRTVLD KAVQADGQVK ECYQSHRDTI VLLCKPEPEL NAAIPSANPA
   541  KTMQGSEVVN VLKSLLSNLD EVKKEREGLE NDLKSVNFDM TSKFLTALAQ DGVINEEALS
   601  VTELDRVYGG LTTKVQESLK KQEGLLKNIQ VSHQEFSKMK QSNNEANLRE EVLKNLATAY
   661  DNFVELVANL KEGTKFYNEL TEILVRFQNK CSDIVFARKT ERDELLKDLQ QSIAREPSAP
   721  SIPTPAYQSS PAGGHAPTPP TPAPRTMPPT KPQPPARPPP PVLPANRAPS ATAPSPVGAG
   781  TAAPAPSQTP GSAPPPQAQG PPYPTYPGYP GYCQMPMPMG YNPYAYGQYN MPYPPVYHQS
   841  PGQAPYPGPQ QPSYPFPQPP QQSYYPQQ

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PDCD6IP can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Cell surface
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.35
Highest tissue expression: 45 nTPM

Expression across tissuesHPA

Tissue

esophagus: 45 nTPM
colon: 44 nTPM
rectum: 39 nTPM
parathyroid gland: 38 nTPM
skin: 38 nTPM
small intestine: 37 nTPM

Single-cell type

esophageal apical cells: 620 nCPM
colonocytes: 328 nCPM
neutrophil progenitors: 325 nCPM
foveolar cells: 310 nCPM
sertoli cells: 281 nCPM
enterocytes: 240 nCPM

Immune cell

non-classical monocyte: 18 nTPM
intermediate monocyte: 18 nTPM
classical monocyte: 14 nTPM
myeloid DC: 12 nTPM
NK-cell: 12 nTPM
memory B-cell: 12 nTPM

Brain region

pons: 47 nTPM
choroid plexus: 41 nTPM
medulla oblongata: 40 nTPM
white matter: 36 nTPM
hypothalamus: 34 nTPM
cerebral cortex: 32 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PDCD6IP.

Disease | AllUniProt

Conditions PDCD6IP is implicated in, by any mechanism.

Microcephaly 29, primary, autosomal recessive (MCPH29) MIM:620047

Disease | GeneticClinVar

1 pathogenic / likely-pathogenic of 140 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Microcephaly 29, primary, autosomal recessive

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.36
gnomAD pLI: 0.71
gnomAD missense Z: 0.98
DepMap mean gene effect: -0.43
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of PDCD6IP in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PDCD6IP as an antibody target. Whether an autoantibody or antibody against PDCD6IP could matter depends on whether native PDCD6IP is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PDCD6IP is annotated at the cell surface, where native PDCD6IP is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.

Annotation status

The present source text does not explicitly label PDCD6IP as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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