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Aliases for ZNF41 Gene

Aliases for ZNF41 Gene

  • Zinc Finger Protein 41 2 3 5
  • Mental Retardation, X-Linked 89 3
  • 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 mental retardation, 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 Aland Island Eye Disease and Non-Syndromic X-Linked Intellectual Disability. Among its related pathways are Gene Expression. GO annotations related to this gene include nucleic acid binding and transcription factor activity, sequence-specific DNA binding. 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

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

Genomics for ZNF41 Gene

Regulatory Elements for ZNF41 Gene

Enhancers for ZNF41 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XF047523 1.5 FANTOM5 Ensembl ENCODE 12.7 -40.5 -40467 1.4 ATF1 CBX3 ARID4B ZNF2 RAD21 ZNF366 RCOR1 ZNF391 CREM KLF13 ZNF41 LINC01560 CDK16 USP11 ELK1 CFP SYN1 SPACA5 NUS1P1 ARAF
GH0XF047514 1.3 FANTOM5 Ensembl ENCODE 13.5 -32.6 -32589 2.4 GTF2F1 TBP TAF1 JUN RFX5 ZNF121 GATA3 RCOR1 FOS TCF7L2 LINC01560 ZNF41 SNORA11C LOC100419232 INE1 UBA1 ZNF674 NDUFB11 CFP ARAF
GH0XF047507 0.8 FANTOM5 13.2 -24.2 -24181 0.5 PKNOX1 ZNF76 SIN3A YY1 ZNF335 ZNF766 ZNF600 CREM ZBTB20 ZNF680 LINC01560 ZNF41 CFP ARAF GC0XP047511
GH0XF047360 1.5 FANTOM5 Ensembl ENCODE 4.3 +121.2 121237 2.5 PKNOX1 RAD21 RFX5 ZNF121 GLIS2 ZNF366 SCRT2 FOS ZNF263 ZNF280D ZNF41 USP11 SYN1 ZNF81 ZNF157 GC0XM047351
GH0XF047380 0.9 Ensembl ENCODE 4.1 +102.0 101985 2.5 HDGF ZNF263 SP3 NRF1 NFXL1 ZFHX2 ZNF512 IKZF1 ZNF341 EGR2 INE1 UBA1 ZNF41 GC0XP047390 ZNF157
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ZNF41 on UCSC Golden Path with GeneCards custom track

Promoters for ZNF41 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000259998 -266 3801 ZFP64 SIN3A YY1 ZNF121 GLIS2 ZNF263 SP3 YY2 ZHX2 MXD4

Genomic Location for ZNF41 Gene

47,444,779 bp from pter
47,483,234 bp from pter
38,456 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

Suggested Antigen Peptide Sequences for ZNF41 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 KRAB domain.
  • Belongs to the krueppel C2H2-type zinc-finger protein family.
  • Contains 18 C2H2-type zinc fingers.
  • Contains 1 KRAB domain.
  • Belongs to the krueppel C2H2-type zinc-finger protein family.
  • Contains 18 C2H2-type zinc fingers.
genes like me logo Genes that share domains with ZNF41: view

Function for ZNF41 Gene

Molecular function for ZNF41 Gene

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

Gene Ontology (GO) - Molecular Function for ZNF41 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding 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

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , 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

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 IEA,IBA --
genes like me logo Genes that share ontologies with ZNF41: view

No data available for SIGNOR curated interactions for ZNF41 Gene

Transcripts for ZNF41 Gene

Unigene Clusters for ZNF41 Gene

Zinc finger protein 41:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry 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 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, PaxDb, 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.
genes like me logo Genes that share expression patterns with ZNF41: view

Primer Products

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 35
  • 99.7 (n)
(Canis familiaris)
Mammalia ZNF41 34
  • 88.83 (n)
(Bos Taurus)
Mammalia ZNF41 34 35
  • 87.03 (n)
fruit fly
(Drosophila melanogaster)
Insecta BG:DS04929.3 36
  • 45 (a)
CG9797 36
  • 40 (a)
CG11247 36
  • 35 (a)
zf30C 36
  • 30 (a)
CG18011 36
  • 24 (a)
(Caenorhabditis elegans)
Secernentea Y55F3AM.14 36
  • 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)

Paralogs for ZNF41 Gene

Paralogs for ZNF41 Gene

(403) SIMAP similar genes for ZNF41 Gene using alignment to 2 proteins: 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 Sequence Context AA Info Type
rs17147624 Likely benign 47,449,396(+) CTCCT(A/C)TGGGT intron-variant, reference, missense
rs34301930 Likely benign 47,449,110(+) TTACC(A/C)TTTCC reference, missense
rs104894955 Uncertain significance 47,449,438(-) AATTC(C/T)TGGAG intron-variant, reference, missense
rs200722932 Uncertain significance 47,449,469(+) AATAG(C/T)CTCAC intron-variant, reference, missense
rs201140907 Uncertain significance 47,456,440(+) AGCAC(G/T)GGGGG intron-variant, splice-acceptor-variant

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

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

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)

Relevant External Links for ZNF41 Gene

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

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

Disorders for ZNF41 Gene

MalaCards: The human disease database

(3) MalaCards diseases for ZNF41 Gene - From: Orphanet and DISEASES

Disorder Aliases PubMed IDs
aland island eye disease
  • forsius-eriksson syndrome
non-syndromic x-linked intellectual disability
  • mrx
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}.

Relevant External Links for ZNF41

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 S.A. … Kalscheuer V.M. (Am. J. Hum. Genet. 2003) 3 4 22 64
  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. (Cytogenet. Cell Genet. 1999) 3 4 22 64
  3. Isolation and expression analysis of a human zinc finger gene (ZNF41) located on the short arm of the X chromosome. (PMID: 2037297) Franze A. … Grimaldi G. (Genomics 1991) 2 3 4 64
  4. XLID-causing mutations and associated genes challenged in light of data from large-scale human exome sequencing. (PMID: 23871722) Piton A. … Mandel J.L. (Am. J. Hum. Genet. 2013) 3 4 64
  5. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross M.T. … Bentley D.R. (Nature 2005) 3 4 64

Products for ZNF41 Gene

Sources for ZNF41 Gene

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