Seroatlas · Human Serome Atlas

PHF5A

PHD finger-like domain-containing protein 5A

Also known as: bK223H9.2, INI, MGC1346, PHF5A_HUMAN, Rds3, SAP14b, SF3b14b, SF3B7

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

Protein identityUniProt · HPA

UniProt accession
Q7RTV0
Gene
PHF5A
Ensembl
ENSG00000100410
Chromosome
22
Canonical length
110 aa
Protein class
Predicted intracellular proteins, Transcription factors
Subcellular location
Nucleoplasm

OverviewNCBI Gene

This gene encodes a subunit of the splicing factor 3b protein complex. Splicing factor 3b, together with splicing factor 3a and a 12S RNA unit, forms the U2 small nuclear ribonucleoproteins complex (U2 snRNP). The splicing factor 3b/3a complex binds pre-mRNA upstream of the intron's branch site in a sequence-independent manner and may anchor the U2 snRNP to the pre-mRNA. The protein encoded by this gene contains a PHD-finger-like domain that is flanked by highly basic N- and C-termini. This protein belongs to the PHD-finger superfamily and may act as a chromatin-associated protein. This gene has several pseudogenes on different chromosomes. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

110 residues, UniProt reviewed canonical sequence.

>Q7RTV0|PHF5A
     1  MAKHHPDLIF CRKQAGVAIG RLCEKCDGKC VICDSYVRPC TLVRICDECN YGSYQGRCVI
    61  CGGPGVSDAY YCKECTIQEK DRDGCPKIVN LGSSKTDLFY ERKKYGFKKR

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PHF5A 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)
0.35
Highest tissue expression
55 nTPM

Expression across tissuesHPA

Tissue

  • bone marrow: 55 nTPM
  • thymus: 49 nTPM
  • tonsil: 39 nTPM
  • skeletal muscle: 36 nTPM
  • lymph node: 33 nTPM
  • spinal cord: 30 nTPM

Single-cell type

  • extravillous trophoblasts: 131 nCPM
  • syncytiotrophoblasts: 127 nCPM
  • migrating cytotrophoblasts: 120 nCPM
  • esophageal basal cells: 111 nCPM
  • cytotrophoblasts: 109 nCPM
  • differentiating spermatogonia: 106 nCPM

Immune cell

  • total PBMC: 59 nTPM
  • eosinophil: 58 nTPM
  • neutrophil: 56 nTPM
  • myeloid DC: 49 nTPM
  • T-reg: 48 nTPM
  • memory B-cell: 48 nTPM

Brain region

  • white matter: 32 nTPM
  • cerebellum: 24 nTPM
  • medulla oblongata: 24 nTPM
  • basal ganglia: 23 nTPM
  • choroid plexus: 22 nTPM
  • spinal cord: 22 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PHF5A.

Disease | GeneticClinVar

3 pathogenic / likely-pathogenic of 15 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

  • PHF5A-related disorder

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)
0.46
gnomAD pLI
0.87
gnomAD missense Z
2.65
DepMap mean gene effect
-2.44
DepMap dependency class
pan

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 6% 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

  • PHF5-like
  • PHF5-like protein

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of PHF5A 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 PHF5A as an antibody target. Whether an autoantibody or antibody against PHF5A could matter depends on whether native PHF5A is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PHF5A 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 PHF5A as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PHF5A. 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).

© 2026 · Seroatlas, Discover Oregon LLC · Terms of use

Loading the interactive Seroatlas protein explorer...