Seroatlas · Human Serome Atlas

VSX1

Visual system homeobox 1

Also known as: PPCD, PPCD1, PPD, VSX1_HUMAN

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

Protein identityUniProt · HPA

UniProt accession
Q9NZR4
Gene
VSX1
Ensembl
ENSG00000100987
Chromosome
20
Canonical length
365 aa
Protein class
Disease related genes, Human disease related genes, Predicted intracellular proteins, Transcription factors
Subcellular location
Nucleoli

OverviewNCBI Gene

The protein encoded by this gene contains a paired-like homeodomain and binds to the core of the locus control region of the red/green visual pigment gene cluster. The encoded protein may regulate expression of the cone opsin genes early in development. Mutations in this gene can cause posterior polymorphous corneal dystrophy and keratoconus. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

365 residues, UniProt reviewed canonical sequence.

>Q9NZR4|VSX1
     1  MTGRDSLSDG RTSSRALVPG GSPRGSRPRG FAITDLLGLE AELPAPAGPG QGSGCEGPAV
    61  APCPGPGLDG SSLARGALPL GLGLLCGFGT QPPAAARAPC LLLADVPFLP PRGPEPAAPL
   121  APSRPPPALG RQKRSDSVST SDEDSQSEDR NDLKASPTLG KRKKRRHRTV FTAHQLEELE
   181  KAFSEAHYPD VYAREMLAVK TELPEDRIQV WFQNRRAKWR KREKRWGGSS VMAEYGLYGA
   241  MVRHCIPLPD SVLNSAEGGL LGSCAPWLLG MHKKSMGMIR KPGSEDKLAG LWGSDHFKEG
   301  SSQSESGSQR GSDKVSPENG LEDVAIDLSS SARQETKKVH PGAGAQGGSN STALEGPQPG
   361  KVGAT

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against VSX1 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
Intracellular
Secreted
No
Transmembrane segments
0
Mean surface accessibility (rSASA)
0.61
Highest tissue expression
33 nTPM

Expression across tissuesHPA

Tissue

  • retina: 33 nTPM
  • cerebellum: 15 nTPM
  • pituitary gland: 2.8 nTPM
  • amygdala: 2.5 nTPM
  • midbrain: 2.4 nTPM
  • hypothalamus: 2.2 nTPM

Single-cell type

  • retinal bipolar cells: 483 nCPM
  • oligodendrocyte progenitor cells: 30 nCPM
  • bergmann glia: 19 nCPM
  • astrocytes: 11 nCPM
  • somatotrophs: 11 nCPM
  • corticotrophs: 10 nCPM

Immune cell

  • basophil: 0.5 nTPM
  • neutrophil: 0.4 nTPM
  • plasmacytoid DC: 0.3 nTPM
  • NK-cell: 0.2 nTPM
  • memory B-cell: 0.1 nTPM
  • naive B-cell: 0.1 nTPM

Brain region

  • cerebellum: 30 nTPM
  • hypothalamus: 6.6 nTPM
  • amygdala: 6.4 nTPM
  • midbrain: 6.4 nTPM
  • thalamus: 6.4 nTPM
  • white matter: 6.3 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about VSX1.

Disease | AllUniProt

Conditions VSX1 is implicated in, by any mechanism.

  • Keratoconus 1 (KTCN1) MIM:148300
  • Craniofacial anomalies and anterior segment dysgenesis syndrome (CAASDS) MIM:614195

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)
0.87
gnomAD pLI
0.04
gnomAD missense Z
0.48
DepMap mean gene effect
0.09
DepMap dependency class
none

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

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads VSX1 as an antibody target. Whether an autoantibody or antibody against VSX1 could matter depends on whether native VSX1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

VSX1 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label VSX1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/VSX1. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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