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Aliases for ZNF41 Gene

Aliases for ZNF41 Gene

  • Zinc Finger Protein 41 2 3 3 5
  • MRX89 3

External Ids for ZNF41 Gene

Previous GeneCards Identifiers for ZNF41 Gene

  • GC0XM046109
  • GC0XM045567
  • GC0XM046353
  • GC0XM046354
  • GC0XM047062
  • GC0XM047190
  • GC0XM047305
  • GC0XM045018

Summaries for ZNF41 Gene

Entrez Gene Summary for ZNF41 Gene

  • This gene encodes a protein that contains KRAB-A and KRAB-B domains multiple zinc finger DNA binding motifs and finger linking regions characteristic of the Kruppel family. An initial study suggested that this gene may be associated with X-linked cognitive disability, but a later study has called this finding into question (PMID:23871722).[provided by RefSeq, Apr 2016]

GeneCards Summary for ZNF41 Gene

ZNF41 (Zinc Finger Protein 41) is a Protein Coding gene. Diseases associated with ZNF41 include Non-Syndromic X-Linked Intellectual Disability and Aland Island Eye Disease. Among its related pathways are Gene Expression. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and DNA binding transcription factor activity. An important paralog of this gene is ZNF484.

UniProtKB/Swiss-Prot for ZNF41 Gene

  • May be involved in transcriptional regulation.

Gene Wiki entry for ZNF41 Gene

Additional gene information for ZNF41 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZNF41 Gene

Genomics for ZNF41 Gene

GeneHancer (GH) Regulatory Elements for ZNF41 Gene

Promoters and enhancers for ZNF41 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ047481 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.7 -0.3 -298 3.5 ATF1 ZFP64 SIN3A YY1 TCF12 GLIS2 ZNF143 ATF7 DEK SP3 LINC01560 ZNF41 INE1 UBA1 ZNF81 TIMP1 ELK1 FTSJ1 ARAF GC0XP047511
GH0XJ047512 Promoter/Enhancer 1.7 EPDnew Ensembl dbSUPER 663.1 -30.2 -30167 1.2 YY1 ZNF324 ZNF335 POLR2A PATZ1 ATF7 PRDM10 ZNF600 ZBTB20 ZBTB10 ZNF41 GC0XP047511 GC0XP047512 NUS1P1 LINC01560
GH0XJ047482 Enhancer 0.4 Ensembl 650.7 +1.7 1733 0.2 ZNF121 ZMYM3 LINC01560 ZNF41 ENSG00000277605
GH0XJ046544 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 9.8 +936.8 936758 4.6 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B ZNF674-AS1 ZNF674 CHST7 LOC100113397 LINC01560 INE1 LOC392452 SLC9A7 NUS1P1 ZNF41
GH0XJ047523 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 12.7 -40.5 -40467 1 ATF1 ARID4B ZNF2 ZNF143 ATF7 RUNX3 DEK SP3 SP5 REST LINC01560 ZNF41 USP11 CDK16 ELK1 CFP SYN1 SPACA5 GC0XP047511 NUS1P1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ZNF41 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ZNF41 gene promoter:
  • AML1a
  • C/EBPalpha
  • RORalpha2
  • POU2F1a
  • POU2F1
  • c-Rel
  • YY1
  • STAT5A
  • Nkx2-5
  • MRF-2

Genomic Locations for ZNF41 Gene

Genomic Locations for ZNF41 Gene
38,456 bases
Minus strand
37,068 bases
Minus strand

Genomic View for ZNF41 Gene

Genes around ZNF41 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZNF41 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZNF41 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZNF41 Gene

Proteins for ZNF41 Gene

  • Protein details for ZNF41 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Zinc finger protein 41
    Protein Accession:
    Secondary Accessions:
    • A8K1V6
    • B4DH01
    • Q96LE8
    • Q9UMC4
    • Q9UMV5
    • Q9UMV6
    • Q9UMV7
    • Q9UMV8
    • Q9UMV9
    • Q9UMW0
    • Q9UMW1

    Protein attributes for ZNF41 Gene

    821 amino acids
    Molecular mass:
    93728 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for ZNF41 Gene

neXtProt entry for ZNF41 Gene

Post-translational modifications for ZNF41 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for ZNF41 Gene

Domains & Families for ZNF41 Gene

Gene Families for ZNF41 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for ZNF41 Gene

Suggested Antigen Peptide Sequences for ZNF41 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the krueppel C2H2-type zinc-finger protein family.
  • Belongs to the krueppel C2H2-type zinc-finger protein family.
genes like me logo Genes that share domains with ZNF41: view

Function for ZNF41 Gene

Molecular function for ZNF41 Gene

UniProtKB/Swiss-Prot Function:
May be involved in transcriptional regulation.
GENATLAS Biochemistry:
zinc finger protein 41 (C2H2 type,Kruppel-like),involved in gene-specific transcriptional repression

Gene Ontology (GO) - Molecular Function for ZNF41 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding ISA --
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IBA --
GO:0005515 protein binding IPI 25416956
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ZNF41: view
genes like me logo Genes that share phenotypes with ZNF41: view

Human Phenotype Ontology for ZNF41 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for ZNF41 Gene

miRTarBase miRNAs that target ZNF41
Targeted motifs for ZNF41 Gene
HOMER Transcription Factor Regulatory Elements motif ZNF41
  • Consensus sequence: CCTCATGGTGYCYTWYTCCCTTGTG Submotif: canonical Cell Type: HEK293 GEO ID: GSE58341

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Animal Models and Transcription Factor Targets for ZNF41 Gene

Localization for ZNF41 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZNF41 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ZNF41 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for ZNF41 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with ZNF41: view

Pathways & Interactions for ZNF41 Gene

SuperPathways for ZNF41 Gene

SuperPathway Contained pathways
1 Gene Expression
genes like me logo Genes that share pathways with ZNF41: view

Pathways by source for ZNF41 Gene

2 Reactome pathways for ZNF41 Gene

Gene Ontology (GO) - Biological Process for ZNF41 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IBA,IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA --
genes like me logo Genes that share ontologies with ZNF41: view

No data available for SIGNOR curated interactions for ZNF41 Gene

Drugs & Compounds for ZNF41 Gene

No Compound Related Data Available

Transcripts for ZNF41 Gene

Unigene Clusters for ZNF41 Gene

Zinc finger protein 41:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZNF41 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b · 7c · 7d · 7e · 7f ^ 8 ^ 9a · 9b · 9c · 9d · 9e
SP1: - - - - - - -
SP2: - - - - - - - - -
SP3: - - -
SP4: -
SP5: - -
SP7: -
SP8: - -
SP9: - - - - - - - - -
SP10: - - - - - -
SP11: - - - - - - - -
SP12: - - - - - -
SP13: - - - -
SP14: - - - - -
SP15: - - - - -

Relevant External Links for ZNF41 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ZNF41 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZNF41 Gene

Protein differential expression in normal tissues from HIPED for ZNF41 Gene

This gene is overexpressed in Platelet (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for ZNF41 Gene

Protein tissue co-expression partners for ZNF41 Gene

NURSA nuclear receptor signaling pathways regulating expression of ZNF41 Gene:


SOURCE GeneReport for Unigene cluster for ZNF41 Gene:


mRNA Expression by UniProt/SwissProt for ZNF41 Gene:

Tissue specificity: Expressed in the heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas.

Evidence on tissue expression from TISSUES for ZNF41 Gene

  • Nervous system(4.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for ZNF41 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • nose
  • outer ear
  • salivary gland
  • skull
  • tooth
  • lung
  • rib
  • rib cage
  • pelvis
  • testicle
  • urinary bladder
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with ZNF41: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for ZNF41 Gene

Orthologs for ZNF41 Gene

This gene was present in the common ancestor of animals.

Orthologs for ZNF41 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ZNF41 34 33
  • 99.7 (n)
(Canis familiaris)
Mammalia ZNF41 33
  • 88.83 (n)
(Bos Taurus)
Mammalia ZNF41 34 33
  • 87.03 (n)
fruit fly
(Drosophila melanogaster)
Insecta BG:DS04929.3 35
  • 45 (a)
CG9797 35
  • 40 (a)
CG11247 35
  • 35 (a)
zf30C 35
  • 30 (a)
CG18011 35
  • 24 (a)
(Caenorhabditis elegans)
Secernentea Y55F3AM.14 35
  • 38 (a)
Species where no ortholog for ZNF41 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • zebrafish (Danio rerio)

Evolution for ZNF41 Gene

Gene Tree for ZNF41 (if available)
Gene Tree for ZNF41 (if available)
Evolutionary constrained regions (ECRs) for ZNF41: view image

Paralogs for ZNF41 Gene

(403) SIMAP similar genes for ZNF41 Gene using alignment to 2 proteins:

  • B1AQ29_HUMAN Pseudogenes for ZNF41 Gene

genes like me logo Genes that share paralogs with ZNF41: view

Variants for ZNF41 Gene

Sequence variations from dbSNP and Humsavar for ZNF41 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1025319944 uncertain-significance, Non-syndromic X-linked intellectual disability 47,482,693(-) G/A 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant
rs104894955 conflicting-interpretations-of-pathogenicity, likely-benign, not provided, Non-syndromic X-linked intellectual disability 47,449,438(-) G/A coding_sequence_variant, intron_variant, missense_variant
rs1057515901 uncertain-significance, Non-syndromic X-linked intellectual disability 47,446,397(-) T/C 3_prime_UTR_variant
rs1057515902 uncertain-significance, Non-syndromic X-linked intellectual disability 47,446,961(-) G/A 3_prime_UTR_variant
rs1057515903 uncertain-significance, Non-syndromic X-linked intellectual disability 47,449,422(-) G/A coding_sequence_variant, intron_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for ZNF41 Gene

Variant ID Type Subtype PubMed ID
esv2664341 CNV deletion 23128226
esv3558856 CNV deletion 23714750

Variation tolerance for ZNF41 Gene

Residual Variation Intolerance Score: 98.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.57; 56.00% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZNF41 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZNF41 Gene

Disorders for ZNF41 Gene

MalaCards: The human disease database

(5) MalaCards diseases for ZNF41 Gene - From: HGMD, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
non-syndromic x-linked intellectual disability
  • non-specific x-linked mental retardation
aland island eye disease
  • aied
syndromic x-linked intellectual disability
  • syndromic intellectual disability, x-linked
x-linked non-specific intellectual disability
  • x-linked non-syndromic intellectual disability
congenital stationary night blindness
  • congenital essential nyctalopia
- elite association - COSMIC cancer census association via MalaCards
Search ZNF41 in MalaCards View complete list of genes associated with diseases


  • Note=A chromosomal aberration involving ZNF41 has been found in a patient with severe mental retardation. Translocation t(X;7)(p11.3;q11.21). {ECO:0000269 PubMed:14628291}.

Additional Disease Information for ZNF41

genes like me logo Genes that share disorders with ZNF41: view

No data available for Genatlas for ZNF41 Gene

Publications for ZNF41 Gene

  1. Mutations in the ZNF41 gene are associated with cognitive deficits: identification of a new candidate for X-linked mental retardation. (PMID: 14628291) Shoichet SA … Kalscheuer VM (American journal of human genetics 2003) 3 4 22 58
  2. Coding region intron/exon organization, alternative splicing, and X-chromosome inactivation of the KRAB/FPB-domain-containing human zinc finger gene ZNF41. (PMID: 10449920) Rosati M … Grimaldi G (Cytogenetics and cell genetics 1999) 3 4 22 58
  3. Isolation and expression analysis of a human zinc finger gene (ZNF41) located on the short arm of the X chromosome. (PMID: 2037297) Franzè A … Grimaldi G (Genomics 1991) 2 3 4 58
  4. XLID-causing mutations and associated genes challenged in light of data from large-scale human exome sequencing. (PMID: 23871722) Piton A … Mandel JL (American journal of human genetics 2013) 3 4 58
  5. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4 58

Products for ZNF41 Gene

Sources for ZNF41 Gene

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