Phenotypic Mutation 'mister_clean' (pdf version)
Allelemister_clean
Mutation Type critical splice donor site (1 bp from exon)
Chromosome14
Coordinate70,797,504 bp (GRCm39)
Base Change G ⇒ A (forward strand)
Gene Hr
Gene Name lysine demethylase and nuclear receptor corepressor
Synonym(s) rh-bmh, rh, N, bldy, ba
Chromosomal Location 70,789,652-70,810,988 bp (+) (GRCm39)
MGI Phenotype FUNCTION: This gene encodes a protein that is involved in hair growth. This protein functions as a transcriptional corepressor of multiple nuclear receptors, including thyroid hormone receptor, the retinoic acid receptor-related orphan receptors and the vitamin D receptors, and it interacts with histone deacetylases. The translation of this protein is modulated by a regulatory ORF that exists upstream of the primary ORF. Mutations in this upstream ORF, U2HR, cause Marie Unna hereditary hypotrichosis (MUHH), an autosomal dominant form of genetic hair loss in human. [provided by RefSeq, Oct 2014]
PHENOTYPE: Mutant homozygotes exhibit hair loss, usually wrinkled skin with epidermal cysts. Females do not nurse their pups well. [provided by MGI curators]
Accession Number
NCBI RefSeq: NM­_021877; MGI: 96223
MappedYes 
Amino Acid Change
Institutional SourceBeutler Lab
Gene Model not available
AlphaFold Q61645
SMART Domains Protein: ENSMUSP00000022691
Gene: ENSMUSG00000022096

DomainStartEndE-ValueType
Blast:JmjC 54 849 N/A BLAST
JmjC 939 1150 5.23e-38 SMART
Predicted Effect probably benign
SMART Domains Protein: ENSMUSP00000124816
Gene: ENSMUSG00000022096

DomainStartEndE-ValueType
Blast:JmjC 54 849 N/A BLAST
JmjC 939 1150 5.23e-38 SMART
Predicted Effect probably benign
SMART Domains Protein: ENSMUSP00000124042
Gene: ENSMUSG00000022096

DomainStartEndE-ValueType
low complexity region 12 21 N/A INTRINSIC
Blast:JmjC 83 878 N/A BLAST
JmjC 968 1179 5.23e-38 SMART
Predicted Effect probably benign
Meta Mutation Damage Score Not available question?
Is this an essential gene? Non Essential (E-score: 0.000) question?
Phenotypic Category Autosomal Recessive
Candidate Explorer Status loading ...
Single pedigree
Linkage Analysis Data
Penetrance 100% 
Alleles Listed at MGI

All alleles(25) : Targeted, knock-out(1) Targeted, other(2) Transgenic(1) Spontaneous(15) Chemically induced(6)

Lab Alleles
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01805:Hr APN 14 70802737 splice site probably benign
IGL02020:Hr APN 14 70793877 missense probably benign 0.01
IGL02372:Hr APN 14 70795790 missense possibly damaging 0.94
IGL02380:Hr APN 14 70795201 missense probably damaging 0.98
IGL02554:Hr APN 14 70797306 splice site probably benign
IGL02949:Hr APN 14 70797225 missense possibly damaging 0.87
IGL03406:Hr APN 14 70800860 critical splice donor site probably null
angie UTSW 14 70805273 missense probably damaging 0.97
blofeld UTSW 14 70805525 missense probably damaging 1.00
general UTSW 14 70801124 critical splice donor site probably null
kaburo UTSW 14 unclassified
mushroom UTSW 14 70805525 missense probably damaging 1.00
prune UTSW 14 70808869 missense probably damaging 1.00
ren UTSW 14 70805525 missense probably damaging 1.00
subclinical UTSW 14 70799276 missense possibly damaging 0.89
vessel UTSW 14 70799305 nonsense probably null
yuanxiao UTSW 14 70808888 missense probably damaging 1.00
R0018:Hr UTSW 14 70795717 missense probably benign
R0038:Hr UTSW 14 70805525 missense probably damaging 1.00
R0374:Hr UTSW 14 70793916 missense probably benign 0.01
R0511:Hr UTSW 14 70799352 nonsense probably null
R0609:Hr UTSW 14 70797097 missense probably benign
R1828:Hr UTSW 14 70809477 critical splice donor site probably null
R2030:Hr UTSW 14 70808888 missense probably damaging 1.00
R2266:Hr UTSW 14 70795547 missense probably benign
R2267:Hr UTSW 14 70795547 missense probably benign
R2268:Hr UTSW 14 70795547 missense probably benign
R2377:Hr UTSW 14 70795318 missense probably damaging 1.00
R3686:Hr UTSW 14 70795236 missense probably damaging 0.98
R3687:Hr UTSW 14 70795236 missense probably damaging 0.98
R3754:Hr UTSW 14 70805264 missense probably damaging 1.00
R3803:Hr UTSW 14 70795333 missense probably benign 0.01
R3846:Hr UTSW 14 70808893 missense probably damaging 1.00
R3977:Hr UTSW 14 70801024 missense probably benign 0.01
R3978:Hr UTSW 14 70801024 missense probably benign 0.01
R3979:Hr UTSW 14 70801024 missense probably benign 0.01
R4528:Hr UTSW 14 70803823 missense probably damaging 1.00
R4654:Hr UTSW 14 70801013 missense probably damaging 0.99
R4834:Hr UTSW 14 70797362 missense probably damaging 0.98
R4847:Hr UTSW 14 70793916 missense probably benign 0.04
R4863:Hr UTSW 14 70809412 missense probably damaging 1.00
R5292:Hr UTSW 14 70809432 missense probably damaging 1.00
R5452:Hr UTSW 14 70794067 missense probably damaging 1.00
R5717:Hr UTSW 14 70803616 missense probably benign 0.34
R5902:Hr UTSW 14 70795231 missense probably benign 0.02
R6000:Hr UTSW 14 70805273 missense probably damaging 0.97
R6439:Hr UTSW 14 70799276 missense possibly damaging 0.89
R6823:Hr UTSW 14 70802814 missense probably damaging 0.98
R7030:Hr UTSW 14 70801124 critical splice donor site probably null
R7213:Hr UTSW 14 70795790 missense probably damaging 0.99
R7452:Hr UTSW 14 70808926 missense probably damaging 1.00
R7468:Hr UTSW 14 70795652 missense possibly damaging 0.89
R7572:Hr UTSW 14 70799293 missense possibly damaging 0.66
R7956:Hr UTSW 14 70797327 missense probably benign
R7996:Hr UTSW 14 70801043 nonsense probably null
R7997:Hr UTSW 14 70801043 nonsense probably null
R8076:Hr UTSW 14 70795381 missense probably benign 0.00
R8101:Hr UTSW 14 70805282 missense possibly damaging 0.67
R8553:Hr UTSW 14 70804965 missense probably damaging 1.00
R8749:Hr UTSW 14 70795510 missense probably damaging 1.00
R8850:Hr UTSW 14 70799305 nonsense probably null
R8949:Hr UTSW 14 70795328 missense probably benign 0.01
R9139:Hr UTSW 14 70795079 missense possibly damaging 0.65
R9236:Hr UTSW 14 70809396 missense probably damaging 1.00
R9246:Hr UTSW 14 70808915 missense probably damaging 1.00
R9327:Hr UTSW 14 70805228 missense possibly damaging 0.91
R9337:Hr UTSW 14 70797324 missense probably benign 0.00
R9487:Hr UTSW 14 70794205 missense possibly damaging 0.77
R9487:Hr UTSW 14 70793877 missense probably benign 0.01
R9700:Hr UTSW 14 70804616 missense probably benign 0.00
X0025:Hr UTSW 14 70804391 splice site probably null
X0026:Hr UTSW 14 70805281 missense probably damaging 0.99
Mode of Inheritance Autosomal Recessive
Local Stock Sperm, gDNA
MMRRC Submission 031039-UCD
Last Updated 2018-03-02 4:47 PM by Diantha La Vine
Record Created unknown
Record Posted 2009-03-05
Phenotypic Description

The mister clean mutant phenotype emerged as a visible variant among G3 mice homozygous for mutations induced by N-ethyl-N-nitrosourea (ENU).  The index mouse was completely hairless by weaning age and exhibited wrinkled skin (Figure 1).  They are phenotypically similar to prune mice, which have a mutation in the hr gene.

Nature of Mutation
Due to the similarity in phenotype with prune mice, the hr locus was directly sequenced and a G to A transition was found in the donor splice site of intron 6 one nucleotide after the last exon (GTGAGC -> ATGAGC) in the hr gene on chromosome 14 (position 6009 in Genbank genomic region NC_000080 for linear genomic DNA sequence of hr).  The mutation may result in skipping of the 191-nucleotide exon 6 (out of 20 total exons) in ENSMUST00000022691, destroying the reading frame in the middle of the encoded HR polypeptide chain (33 aberrant amino acids after position 515), and creating a premature stop codon that would truncate the protein after amino acid 548.  The effect of the mutation at the cDNA and protein level has not been tested.
 
       <--exon 5  <--exon 6 intron 6-->  exon 7-->   <--exon 7
5724 AAATCACGTAG……AGCGAGAAG GTGAGCCAA…………GCCAGGGGCC……CCACTGTAG 7859
512  -K--S--R--………Q--R--E--             R--P--G--A-……-P--L--*  548
      correct     deleted                       aberrant
 
The donor splice site of intron 6, which is destroyed by the mister clean mutation, is indicated in blue lettering; the mutated nucleotide is indicated in red lettering.
 
In the ENSMUST00000163060 transcript, the mutation corresponds to the donor splice site of intron 4. The mutation may result in skipping of the 191-nucleotide exon 4 (out of 18 total exons), destroying the reading frame in the middle of the encoded HR polypeptide chain (33 aberrant amino acids after position 515), and creating a premature stop codon that would truncate the protein after amino acid 642. 
 
       <--exon 3  <--exon 4 intron 4-->  exon 5-->   <--exon 5
1621 AAATCACGTAG……AGCGAGAAG GTGAGCCAA…………GCCAGGGGCC……CCACTGTAG 1925
541  -K--S--R--………Q--R--E--             R--P--G--A-……-P--L--*  642
      correct     deleted                       aberrant
Illustration of Mutations in
Gene & Protein
Protein Prediction

Figure 2. HR functional domains. The N-terminal domain varies between the two isoforms of HR; only the longer isoform is shown. The position of the mister clean mutation is indiated in red and results in a G to A transition in the donor splice site of intron 4 of the isoform encoded by the cDNA transcript ENSMUST00000163060, or at donor splice site of intron 6 of the isoform encoded by the ENSMUST00000022691 cDNA transcript (not shown). NMTS, nuclear matrix targeting signal; RD, repression domain; NLS, nuclear localization signal; ID, interacting domain; ZF, zinc finger domain; ROR, retinoic acid receptor related orphan receptor; TR, thyroid hormone receptor. Click on the image to view other mutations found in HR. Click on each mutation for more specific information.

The mister clean mutation likely results in the loss or weakening of the normal donor splice site of intron 4, which may lead to skipping of exon 4, a frame shift and premature truncation after the addition of 33 aberrant amino acids (Figure 2).  Exon 4 does not encode any defined portion of the HR protein.  Truncation occurs after the localization sequences and the first repressor domain.  If the truncated protein was expressed, it would be missing the zinc finger, the JmjC domain, as well as two defined repression domains and nuclear receptor interacting motifs.

Please see the record for prune for more information about Hairless.
Putative Mechanism
The phenotype of hr alleles is correlated with genotype.  Thus, classical hairless mice that exhibit hairlessness, but not thickened and wrinkled skin, typically express some level of functional protein, while animals with severe versions of the rhino phenotype do not.  The mister clean mutation is predicted to result in truncation of the HR protein, similar to some of the rhino alleles (1).  Although mister clean mutants display some thickening and wrinkling of the skin, their phenotypes do not appear as severe as prune or knockout hr animals suggesting that some correct or alternative splicing may occur in these animals along with the retention of some HR function. 
Primers Primers cannot be located by automatic search.
Genotyping
Mister clean genotyping is performed by amplifying the region containing the mutation using PCR, followed by sequencing of the amplified region to detect the single nucleotide change.  
 
Primers for PCR amplification
MrClean(F): 5’- CCATCCGTCCACGTTGGAATCATC -3’
MrClean(R): 5’- TGCACTGGCTGTTTCCTCCATAAG -3’
 
PCR program (use SIGMA JumpStart REDTaq)
1) 94°C             2:00
2) 94°C             0:30
3) 56°C             0:30
4) 72°C             1:00
5) repeat steps (2-4) 29X
6) 72°C             7:00
7) 4°C               ∞
 
Primers for sequencing
MrClean_seq(F1): 5’- CTTCCTAGAGACTTGGGCTGAAC -3'
MrClean_seq(F2): 5’- AGACTTGTGGATACATCCTGC -3’
MrClean_seq(R): 5’- GACTGGACCAAGTCTTTAGACTC -3’
 
The following sequence of 1033 nucleotides (from Genbank genomic region NC_000080 for linear DNA sequence of hr) is amplified:
 
5210                                                      c catccgtcca
5221 cgttggaatc atctcacagt gtcacatagc cacttagcct ttagctgacc tacccaaagt
5281 ctatactggc tggattctgc acgtgtacaa ggaccattgc tcaggcttcc tagagacttg
5341 ggctgaacat gctaaacaac ccctgagcct ccattcctac cagggacatc tccagctact
5401 gctcagcttt gtgtgtgaaa tatactggac tgatcctctt tcgggttctg aattggtcct
5461 cacaagcctg gggtccaggg gctgaattgg ctgcatgtgg acaagggtgg gtgttaattc
5521 agggctttga ctagcataag ccccagaaac cagactccct aagcaactgt attgtctccc
5581 cagggccccg agatggcagg attaggctcc aggagtccag acttgtggat acatcctgcc
5641 agcatcactt agcaggtgtc acccagtgcc aaagctgtgt ccaggcagct ggagaggtag
5701 gggtactgac cggccactcc cagaaatcac gtaggtgagt gttgtgtctg acagtcagag
5761 ccagcagcac tccatcccca cccaggggct ccctcctcaa gcttcatcca tttccaggtc
5821 acccctggag gagaagcagt tggaggagga ggattcctct gccacttccg aagaaggagg
5881 aggagggcct ggcccagaag cttcactcaa caagggcctg gccaagcacc tgctgagtgg
5941 tttgggggac cgactctgcc gcctgctgcg gaaggagcgg gaggcccttg cctgggcaca
6001 gcgagaaggt gagccaattt cccttgtggg cctgctcctg catgtccctc ccaacccacg
6061 tttaccagtg ctttggggtt cccaggccta ctcaggagag ctccgtcctt ctttgttcct
6121 agctatccct agcacggact cttggtcaat cctgaggttt ctggcctcct ggggagtcta
6181 aagacttggt ccagtctagt tctctaagaa caactgggct tatggaggaa acagccagtg
6241 ca
 
PCR primer binding sites are underlined; sequencing primer binding sites are highlighted in gray; the mutated G is shown in red text.
References

  1.  Cachon-Gonzalez, M. B., San-Jose, I., Cano, A., Vega, J. A., Garcia, N., Freeman, T., Schimmang, T., and Stoye, J. P. (1999) The hairless gene of the mouse: relationship of phenotypic effects with expression profile and genotype, Dev. Dyn. 216, 113-126.

Science Writers Nora G. Smart
Illustrators Diantha La Vine
AuthorsXin Du, Bruce Beutler
Edit History
2011-01-07 9:22 AM (current)
2010-11-08 11:14 AM
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