Incidental Mutation 'R5272:Crx'
ID 400409
Institutional Source Beutler Lab
Gene Symbol Crx
Ensembl Gene ENSMUSG00000041578
Gene Name cone-rod homeobox
Synonyms Crx1
MMRRC Submission 042836-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.375) question?
Stock # R5272 (G1)
Quality Score 225
Status Not validated
Chromosome 7
Chromosomal Location 15599872-15613880 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 15602210 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Tyrosine at position 156 (C156Y)
Ref Sequence ENSEMBL: ENSMUSP00000134400 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000044434] [ENSMUST00000132563] [ENSMUST00000172758] [ENSMUST00000174318]
AlphaFold O54751
Predicted Effect probably damaging
Transcript: ENSMUST00000044434
AA Change: C132Y

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000043436
Gene: ENSMUSG00000041578
AA Change: C132Y

DomainStartEndE-ValueType
HOX 39 101 2.39e-24 SMART
low complexity region 139 153 N/A INTRINSIC
Pfam:TF_Otx 164 250 1.1e-15 PFAM
internal_repeat_1 260 278 1.41e-5 PROSPERO
internal_repeat_1 279 296 1.41e-5 PROSPERO
Predicted Effect probably damaging
Transcript: ENSMUST00000132563
AA Change: C132Y

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000133833
Gene: ENSMUSG00000041578
AA Change: C132Y

DomainStartEndE-ValueType
HOX 39 101 2.39e-24 SMART
low complexity region 139 153 N/A INTRINSIC
low complexity region 196 207 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000172758
SMART Domains Protein: ENSMUSP00000134463
Gene: ENSMUSG00000041578

DomainStartEndE-ValueType
HOX 39 74 6.07e-1 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000174318
AA Change: C156Y

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000134400
Gene: ENSMUSG00000041578
AA Change: C156Y

DomainStartEndE-ValueType
HOX 39 101 2.39e-24 SMART
low complexity region 139 153 N/A INTRINSIC
Pfam:TF_Otx 164 250 1.1e-15 PFAM
internal_repeat_1 260 278 1.41e-5 PROSPERO
internal_repeat_1 279 296 1.41e-5 PROSPERO
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174358
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.4%
  • 20x: 93.0%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a photoreceptor-specific transcription factor which plays a role in the differentiation of photoreceptor cells. This homeodomain protein is necessary for the maintenance of normal cone and rod function. Mutations in this gene are associated with photoreceptor degeneration, Leber congenital amaurosis type III and the autosomal dominant cone-rod dystrophy 2. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some variants has not been determined. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit a lack of photoreceptor outer segments and rod and cone activity, reduced expression of several photoreceptor- and pineal-specific genes, and altered circadian behavior. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 44 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Actl6a A G 3: 32,772,759 (GRCm39) E245G probably damaging Het
Arsb A T 13: 93,930,670 (GRCm39) T213S possibly damaging Het
Cep152 G A 2: 125,452,950 (GRCm39) T374I probably benign Het
Csmd1 T A 8: 16,249,958 (GRCm39) T1007S probably damaging Het
Cyp19a1 A T 9: 54,083,898 (GRCm39) C164S probably benign Het
Ddx55 A T 5: 124,696,092 (GRCm39) I137F possibly damaging Het
Dgkg C A 16: 22,407,044 (GRCm39) probably null Het
Dicer1 A G 12: 104,670,499 (GRCm39) I1022T probably damaging Het
Dis3l2 T C 1: 86,901,126 (GRCm39) V439A possibly damaging Het
Dnah5 T C 15: 28,350,811 (GRCm39) V2611A probably benign Het
Dnah6 A G 6: 73,104,844 (GRCm39) probably null Het
Ercc6 A T 14: 32,240,985 (GRCm39) K170* probably null Het
Fibcd1 A T 2: 31,706,635 (GRCm39) C399S probably damaging Het
Fibcd1 G T 2: 31,706,636 (GRCm39) N398K probably damaging Het
Fnbp4 G A 2: 90,583,459 (GRCm39) M327I probably benign Het
Fryl A T 5: 73,222,479 (GRCm39) L256* probably null Het
Galr1 T A 18: 82,423,761 (GRCm39) Y172F probably benign Het
Gpi1 T C 7: 33,920,115 (GRCm39) N186S probably damaging Het
Kcnh8 A G 17: 53,212,043 (GRCm39) I614V probably damaging Het
Krt23 A T 11: 99,369,099 (GRCm39) I398N probably damaging Het
Mia3 G A 1: 183,109,125 (GRCm39) R656* probably null Het
Mup6 G C 4: 60,005,922 (GRCm39) G138A probably damaging Het
Nectin3 A G 16: 46,268,839 (GRCm39) V521A possibly damaging Het
Nhsl3 T C 4: 129,118,005 (GRCm39) T208A possibly damaging Het
Nphs1 A G 7: 30,181,067 (GRCm39) E1096G possibly damaging Het
Or8s5 G A 15: 98,238,246 (GRCm39) A208V probably benign Het
Panx1 C T 9: 14,956,152 (GRCm39) probably null Het
Pcdhb4 A G 18: 37,440,819 (GRCm39) Y43C probably benign Het
Plbd1 A G 6: 136,617,156 (GRCm39) Y62H probably damaging Het
Rab40b A G 11: 121,248,134 (GRCm39) V190A probably damaging Het
Ryr3 T C 2: 112,483,558 (GRCm39) E4063G probably damaging Het
Smlr1 T C 10: 25,411,925 (GRCm39) I21V probably benign Het
Tenm4 T A 7: 96,523,410 (GRCm39) Y1614N probably damaging Het
Tesmin C A 19: 3,456,992 (GRCm39) A257E probably damaging Het
Tgif1 A G 17: 71,153,249 (GRCm39) L34P probably damaging Het
Ticrr C A 7: 79,319,353 (GRCm39) T446K probably benign Het
Tmc7 A G 7: 118,160,276 (GRCm39) I187T probably benign Het
Tpst2 T A 5: 112,455,818 (GRCm39) V119E probably damaging Het
Trf A T 9: 103,105,177 (GRCm39) M45K probably damaging Het
Trim45 T C 3: 100,837,235 (GRCm39) C524R probably damaging Het
Ttc27 G A 17: 75,049,972 (GRCm39) V293I probably damaging Het
Ugt1a6b C T 1: 88,034,949 (GRCm39) R96C possibly damaging Het
Vit A G 17: 78,894,264 (GRCm39) Q222R probably benign Het
Zfp148 T A 16: 33,316,594 (GRCm39) V380D probably damaging Het
Other mutations in Crx
AlleleSourceChrCoordTypePredicted EffectPPH Score
Typhlotic UTSW 7 15,602,032 (GRCm39) nonsense probably null
R0437:Crx UTSW 7 15,605,071 (GRCm39) nonsense probably null
R0729:Crx UTSW 7 15,605,058 (GRCm39) splice site probably benign
R1601:Crx UTSW 7 15,601,736 (GRCm39) splice site probably null
R1898:Crx UTSW 7 15,602,148 (GRCm39) missense probably damaging 1.00
R1933:Crx UTSW 7 15,602,301 (GRCm39) nonsense probably null
R1988:Crx UTSW 7 15,603,272 (GRCm39) missense possibly damaging 0.95
R5326:Crx UTSW 7 15,602,262 (GRCm39) missense probably damaging 1.00
R5542:Crx UTSW 7 15,602,262 (GRCm39) missense probably damaging 1.00
R6134:Crx UTSW 7 15,602,032 (GRCm39) nonsense probably null
R7313:Crx UTSW 7 15,601,857 (GRCm39) missense probably damaging 1.00
R8458:Crx UTSW 7 15,602,031 (GRCm39) missense possibly damaging 0.56
R9619:Crx UTSW 7 15,602,185 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- TCATGGCATAAGGGGCTGAG -3'
(R):5'- GGGTCTTACCATCAGCTTTGTC -3'

Sequencing Primer
(F):5'- CTGAGGTGAGAGAGGGCCC -3'
(R):5'- GGCATGTGAGTTCACTCCC -3'
Posted On 2016-07-06