Incidental Mutation 'R3839:Cdh9'
ID 277072
Institutional Source Beutler Lab
Gene Symbol Cdh9
Ensembl Gene ENSMUSG00000025370
Gene Name cadherin 9
Synonyms T1-cadherin
MMRRC Submission 040892-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.108) question?
Stock # R3839 (G1)
Quality Score 225
Status Validated
Chromosome 15
Chromosomal Location 16728842-16857180 bp(+) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) G to T at 16823524 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Stop codon at position 169 (E169*)
Ref Sequence ENSEMBL: ENSMUSP00000154022 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026432] [ENSMUST00000228307]
AlphaFold no structure available at present
Predicted Effect probably null
Transcript: ENSMUST00000026432
AA Change: E169*
SMART Domains Protein: ENSMUSP00000026432
Gene: ENSMUSG00000025370
AA Change: E169*

DomainStartEndE-ValueType
signal peptide 1 21 N/A INTRINSIC
CA 75 156 2.84e-15 SMART
CA 180 265 5.63e-28 SMART
CA 289 381 1.12e-13 SMART
CA 404 485 8.03e-24 SMART
CA 508 595 1.34e-2 SMART
transmembrane domain 613 635 N/A INTRINSIC
Pfam:Cadherin_C 638 782 1.5e-54 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000228307
AA Change: E169*
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.8%
  • 10x: 97.8%
  • 20x: 96.4%
Validation Efficiency 98% (48/49)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a type II classical cadherin from the cadherin superfamily, integral membrane proteins that mediate calcium-dependent cell-cell adhesion. Mature cadherin proteins are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. The extracellular domain consists of 5 subdomains, each containing a cadherin motif, and appears to determine the specificity of the protein's homophilic cell adhesion activity. Type II (atypical) cadherins are defined based on their lack of a HAV cell adhesion recognition sequence specific to type I cadherins. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous knockout results in the formation of abnormal axonal arbors in some retinal type 5 bipolar cells. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 46 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700028I16Rik A G 10: 82,648,219 (GRCm39) noncoding transcript Het
Abraxas2 T A 7: 132,484,867 (GRCm39) S303R probably benign Het
Ackr3 G A 1: 90,141,850 (GRCm39) S103N probably damaging Het
Arhgef25 T C 10: 127,025,605 (GRCm39) T12A probably benign Het
Aspm C T 1: 139,405,792 (GRCm39) H1560Y probably benign Het
Atg10 A T 13: 91,085,499 (GRCm39) I150K probably damaging Het
AW551984 T C 9: 39,509,204 (GRCm39) probably benign Het
Cald1 A T 6: 34,722,700 (GRCm39) D122V probably damaging Het
Cc2d2a T C 5: 43,876,056 (GRCm39) V1011A probably benign Het
Cmbl T C 15: 31,582,144 (GRCm39) V47A probably damaging Het
Col9a2 C G 4: 120,911,455 (GRCm39) R599G probably damaging Het
Ctnnd2 T A 15: 31,009,174 (GRCm39) probably null Het
Cyp4a10 A C 4: 115,382,544 (GRCm39) E278A possibly damaging Het
Ddx56 T C 11: 6,217,712 (GRCm39) D3G probably benign Het
Dnajb2 G A 1: 75,218,124 (GRCm39) probably null Het
Eif3d T A 15: 77,848,300 (GRCm39) T211S probably benign Het
Fam13c C T 10: 70,378,478 (GRCm39) S336L probably damaging Het
Garnl3 C T 2: 32,879,558 (GRCm39) G923S probably benign Het
Gcnt4 A T 13: 97,083,522 (GRCm39) R273* probably null Het
Gldc T A 19: 30,096,075 (GRCm39) probably benign Het
Glra2 C T X: 164,072,612 (GRCm39) V85I probably benign Het
Gm10608 CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 9: 118,989,784 (GRCm39) probably null Het
Gpam T C 19: 55,068,890 (GRCm39) N450S probably benign Het
Gpr156 T A 16: 37,808,962 (GRCm39) V228D probably damaging Het
Hivep2 C A 10: 14,004,713 (GRCm39) T437K probably benign Het
Hmgcr A G 13: 96,795,597 (GRCm39) I324T probably benign Het
Itga3 A G 11: 94,948,095 (GRCm39) probably null Het
Itih1 T A 14: 30,657,785 (GRCm39) N429Y probably damaging Het
Klhl40 A G 9: 121,609,482 (GRCm39) Y453C possibly damaging Het
Mid1ip1 T C X: 10,584,620 (GRCm39) V51A possibly damaging Het
Msn C A X: 95,203,805 (GRCm39) Q303K probably damaging Het
Nap1l1 T A 10: 111,331,183 (GRCm39) probably null Het
Rala A T 13: 18,067,759 (GRCm39) C91S probably damaging Het
Rps9 A G 7: 3,709,823 (GRCm39) probably benign Het
Sdr16c5 C A 4: 4,006,601 (GRCm39) M230I probably damaging Het
Sec14l3 A G 11: 4,021,544 (GRCm39) probably null Het
Senp2 T C 16: 21,828,485 (GRCm39) S32P probably damaging Het
Skor1 A C 9: 63,051,730 (GRCm39) S746R probably damaging Het
Slc17a4 C T 13: 24,085,752 (GRCm39) R387H probably benign Het
Slc47a1 G T 11: 61,243,884 (GRCm39) probably benign Het
Slit3 A T 11: 35,399,064 (GRCm39) N143I probably benign Het
Tpbg T C 9: 85,725,167 (GRCm39) probably benign Het
Tubb2a G T 13: 34,259,294 (GRCm39) N165K probably benign Het
Usp14 A G 18: 10,024,532 (GRCm39) probably null Het
Vmn2r109 A G 17: 20,774,704 (GRCm39) V217A probably damaging Het
Zfp108 A G 7: 23,959,981 (GRCm39) I191V probably benign Het
Other mutations in Cdh9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00429:Cdh9 APN 15 16,828,448 (GRCm39) missense probably damaging 1.00
IGL00555:Cdh9 APN 15 16,823,492 (GRCm39) missense probably damaging 1.00
IGL01110:Cdh9 APN 15 16,856,012 (GRCm39) missense possibly damaging 0.63
IGL01432:Cdh9 APN 15 16,831,033 (GRCm39) missense probably damaging 1.00
IGL01768:Cdh9 APN 15 16,778,311 (GRCm39) missense possibly damaging 0.51
IGL02043:Cdh9 APN 15 16,856,318 (GRCm39) missense probably damaging 1.00
IGL02304:Cdh9 APN 15 16,848,687 (GRCm39) missense probably benign 0.01
IGL02380:Cdh9 APN 15 16,856,086 (GRCm39) missense possibly damaging 0.79
IGL02505:Cdh9 APN 15 16,856,075 (GRCm39) missense probably damaging 1.00
IGL02675:Cdh9 APN 15 16,849,162 (GRCm39) splice site probably null
IGL02679:Cdh9 APN 15 16,832,316 (GRCm39) missense probably damaging 0.97
IGL03288:Cdh9 APN 15 16,856,135 (GRCm39) missense probably damaging 1.00
R0426:Cdh9 UTSW 15 16,823,540 (GRCm39) critical splice donor site probably null
R0726:Cdh9 UTSW 15 16,831,130 (GRCm39) missense probably benign 0.00
R1335:Cdh9 UTSW 15 16,850,878 (GRCm39) missense probably benign 0.00
R1368:Cdh9 UTSW 15 16,848,568 (GRCm39) splice site probably benign
R1766:Cdh9 UTSW 15 16,778,392 (GRCm39) missense probably damaging 1.00
R1916:Cdh9 UTSW 15 16,823,361 (GRCm39) missense probably benign 0.03
R2325:Cdh9 UTSW 15 16,778,286 (GRCm39) missense probably benign
R2424:Cdh9 UTSW 15 16,850,440 (GRCm39) missense probably damaging 1.00
R3104:Cdh9 UTSW 15 16,855,900 (GRCm39) missense probably damaging 1.00
R3837:Cdh9 UTSW 15 16,823,524 (GRCm39) nonsense probably null
R4241:Cdh9 UTSW 15 16,849,165 (GRCm39) critical splice acceptor site probably null
R4248:Cdh9 UTSW 15 16,850,474 (GRCm39) missense probably benign 0.00
R4576:Cdh9 UTSW 15 16,832,325 (GRCm39) missense possibly damaging 0.73
R4679:Cdh9 UTSW 15 16,851,045 (GRCm39) missense probably benign
R4896:Cdh9 UTSW 15 16,778,242 (GRCm39) missense probably benign 0.12
R4961:Cdh9 UTSW 15 16,850,914 (GRCm39) missense probably benign
R5050:Cdh9 UTSW 15 16,778,233 (GRCm39) missense probably benign 0.12
R5089:Cdh9 UTSW 15 16,778,362 (GRCm39) missense probably damaging 1.00
R5268:Cdh9 UTSW 15 16,851,099 (GRCm39) missense probably benign
R5567:Cdh9 UTSW 15 16,855,930 (GRCm39) missense probably damaging 1.00
R5646:Cdh9 UTSW 15 16,823,371 (GRCm39) missense probably damaging 1.00
R5894:Cdh9 UTSW 15 16,832,186 (GRCm39) missense possibly damaging 0.47
R6440:Cdh9 UTSW 15 16,823,509 (GRCm39) missense probably benign 0.01
R6441:Cdh9 UTSW 15 16,823,509 (GRCm39) missense probably benign 0.01
R7225:Cdh9 UTSW 15 16,856,159 (GRCm39) missense probably damaging 1.00
R7247:Cdh9 UTSW 15 16,778,341 (GRCm39) missense probably damaging 1.00
R7593:Cdh9 UTSW 15 16,823,261 (GRCm39) missense probably damaging 1.00
R7615:Cdh9 UTSW 15 16,856,316 (GRCm39) missense probably damaging 1.00
R7632:Cdh9 UTSW 15 16,851,115 (GRCm39) splice site probably null
R7991:Cdh9 UTSW 15 16,828,489 (GRCm39) missense probably damaging 1.00
R8035:Cdh9 UTSW 15 16,831,152 (GRCm39) missense probably damaging 0.97
R8834:Cdh9 UTSW 15 16,850,964 (GRCm39) missense probably damaging 1.00
R8909:Cdh9 UTSW 15 16,848,610 (GRCm39) missense probably damaging 1.00
R8936:Cdh9 UTSW 15 16,831,162 (GRCm39) critical splice donor site probably null
R8973:Cdh9 UTSW 15 16,831,131 (GRCm39) missense possibly damaging 0.78
R9138:Cdh9 UTSW 15 16,823,273 (GRCm39) missense probably damaging 1.00
R9305:Cdh9 UTSW 15 16,832,138 (GRCm39) missense probably damaging 1.00
RF006:Cdh9 UTSW 15 16,855,916 (GRCm39) missense probably damaging 0.97
X0062:Cdh9 UTSW 15 16,848,625 (GRCm39) missense possibly damaging 0.81
Z1177:Cdh9 UTSW 15 16,850,450 (GRCm39) missense probably benign 0.16
Predicted Primers PCR Primer
(F):5'- ACGCTGCAAAGAGACTAGAC -3'
(R):5'- CTGCCATTGGAATCAAACAACTTC -3'

Sequencing Primer
(F):5'- GAGACTAGACAGAGAAGAAAAATCTC -3'
(R):5'- CTGAGAGGGCATATGGAATC -3'
Posted On 2015-04-06