Incidental Mutation 'R3903:Cdh6'
ID 309277
Institutional Source Beutler Lab
Gene Symbol Cdh6
Ensembl Gene ENSMUSG00000039385
Gene Name cadherin 6
Synonyms K-cadherin, cad6
MMRRC Submission 040907-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.204) question?
Stock # R3903 (G1)
Quality Score 225
Status Validated
Chromosome 15
Chromosomal Location 13028787-13173761 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 13042661 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Lysine to Arginine at position 499 (K499R)
Ref Sequence ENSEMBL: ENSMUSP00000037113 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000036439]
AlphaFold P97326
PDB Structure Crystal structure of cadherin-6 EC12 W4A [X-RAY DIFFRACTION]
Predicted Effect probably benign
Transcript: ENSMUST00000036439
AA Change: K499R

PolyPhen 2 Score 0.386 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000037113
Gene: ENSMUSG00000039385
AA Change: K499R

DomainStartEndE-ValueType
CA 76 157 7e-15 SMART
CA 181 266 9.06e-32 SMART
CA 290 382 1.14e-19 SMART
CA 405 486 8.81e-21 SMART
CA 509 596 2.82e-10 SMART
transmembrane domain 614 636 N/A INTRINSIC
Pfam:Cadherin_C 639 783 5.6e-57 PFAM
Meta Mutation Damage Score 0.0653 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.5%
Validation Efficiency 100% (32/32)
MGI Phenotype FUNCTION: This gene encodes a member of the cadherin family of calcium-dependent glycoproteins that mediate cell adhesion and regulate many morphogenetic events during development. The encoded preproprotein is further processed to generate a mature protein. Mice lacking the encoded protein exhibit delay in mesenchyme-to-epithelial conversion and a loss of nephrons. Multiple distinct genes of the cadherin family, including this gene, are found on chromosome 15. [provided by RefSeq, Oct 2015]
PHENOTYPE: Mice homozygous for a null allele exhibit delayed mesenchyme to epithelial conversion and loss of nephrons. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 30 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Amd1 C T 10: 40,166,453 (GRCm39) R210H probably benign Het
Amt C T 9: 108,174,420 (GRCm39) R62C possibly damaging Het
Ap3m1 T C 14: 21,086,732 (GRCm39) Y185C probably null Het
Calcrl T A 2: 84,198,986 (GRCm39) probably benign Het
Ccdc178 C T 18: 22,156,152 (GRCm39) V573I possibly damaging Het
Col1a2 G A 6: 4,518,822 (GRCm39) probably benign Het
Col6a1 C T 10: 76,547,175 (GRCm39) R730H unknown Het
Cyp4f40 C A 17: 32,878,598 (GRCm39) R47S possibly damaging Het
Eif4a2 AG A 16: 22,929,390 (GRCm39) probably null Het
Fsip2l T C X: 47,930,421 (GRCm39) N649S possibly damaging Het
Gm8180 T A 14: 44,021,092 (GRCm39) R39W probably null Het
Golm1 T C 13: 59,786,154 (GRCm39) Q346R probably damaging Het
Grap T G 11: 61,551,151 (GRCm39) probably null Het
Hormad2 A G 11: 4,377,237 (GRCm39) probably benign Het
Hyal1 T C 9: 107,456,171 (GRCm39) probably null Het
Kif12 A G 4: 63,086,213 (GRCm39) V378A possibly damaging Het
Lrrk2 G A 15: 91,631,904 (GRCm39) S1276N probably damaging Het
Lrrk2 A T 15: 91,631,903 (GRCm39) S1276C probably damaging Het
Obscn T C 11: 59,022,472 (GRCm39) R758G possibly damaging Het
Or4f53 A T 2: 111,088,114 (GRCm39) Y218F probably damaging Het
Or7c70 T G 10: 78,683,132 (GRCm39) I206L probably benign Het
Or8c20 C T 9: 38,260,954 (GRCm39) Q186* probably null Het
Pabpc6 T C 17: 9,888,083 (GRCm39) E156G probably benign Het
Rorb A G 19: 18,939,463 (GRCm39) Y155H probably damaging Het
Samd9l T A 6: 3,376,830 (GRCm39) K144* probably null Het
Scn1a A G 2: 66,148,476 (GRCm39) I3T probably benign Het
Serpinb9 T C 13: 33,194,793 (GRCm39) M183T possibly damaging Het
Wnk1 A G 6: 119,926,012 (GRCm39) S1151P probably damaging Het
Xirp2 C T 2: 67,338,380 (GRCm39) T207I probably benign Het
Zfp39 T C 11: 58,781,001 (GRCm39) Y587C probably benign Het
Other mutations in Cdh6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00560:Cdh6 APN 15 13,034,445 (GRCm39) nonsense probably null
IGL00675:Cdh6 APN 15 13,041,525 (GRCm39) missense possibly damaging 0.80
IGL01063:Cdh6 APN 15 13,064,581 (GRCm39) missense probably damaging 1.00
IGL01335:Cdh6 APN 15 13,051,395 (GRCm39) missense probably benign 0.40
IGL01351:Cdh6 APN 15 13,034,326 (GRCm39) missense possibly damaging 0.55
IGL02010:Cdh6 APN 15 13,034,276 (GRCm39) utr 3 prime probably benign
IGL02428:Cdh6 APN 15 13,064,516 (GRCm39) missense possibly damaging 0.94
PIT4651001:Cdh6 UTSW 15 13,044,805 (GRCm39) missense possibly damaging 0.69
R0124:Cdh6 UTSW 15 13,034,410 (GRCm39) missense probably damaging 1.00
R0256:Cdh6 UTSW 15 13,053,868 (GRCm39) splice site probably benign
R0696:Cdh6 UTSW 15 13,051,418 (GRCm39) missense probably benign 0.36
R1017:Cdh6 UTSW 15 13,051,562 (GRCm39) missense probably benign 0.06
R1240:Cdh6 UTSW 15 13,057,541 (GRCm39) missense possibly damaging 0.48
R1444:Cdh6 UTSW 15 13,091,924 (GRCm39) missense probably benign 0.00
R2008:Cdh6 UTSW 15 13,051,562 (GRCm39) missense possibly damaging 0.74
R2050:Cdh6 UTSW 15 13,057,587 (GRCm39) missense probably benign
R2507:Cdh6 UTSW 15 13,041,447 (GRCm39) missense probably benign 0.10
R3082:Cdh6 UTSW 15 13,044,838 (GRCm39) missense probably damaging 1.00
R3083:Cdh6 UTSW 15 13,044,838 (GRCm39) missense probably damaging 1.00
R4591:Cdh6 UTSW 15 13,051,572 (GRCm39) missense possibly damaging 0.69
R4859:Cdh6 UTSW 15 13,051,418 (GRCm39) missense probably benign 0.36
R4898:Cdh6 UTSW 15 13,034,774 (GRCm39) missense probably damaging 0.99
R5242:Cdh6 UTSW 15 13,064,497 (GRCm39) missense probably benign 0.05
R5313:Cdh6 UTSW 15 13,034,723 (GRCm39) missense probably damaging 1.00
R5545:Cdh6 UTSW 15 13,041,235 (GRCm39) missense probably damaging 1.00
R6360:Cdh6 UTSW 15 13,041,546 (GRCm39) missense possibly damaging 0.82
R6650:Cdh6 UTSW 15 13,051,487 (GRCm39) missense probably benign 0.11
R6830:Cdh6 UTSW 15 13,044,860 (GRCm39) missense probably benign 0.01
R7369:Cdh6 UTSW 15 13,042,724 (GRCm39) missense probably damaging 0.99
R7506:Cdh6 UTSW 15 13,034,396 (GRCm39) missense probably damaging 1.00
R8121:Cdh6 UTSW 15 13,044,757 (GRCm39) missense probably damaging 1.00
R8801:Cdh6 UTSW 15 13,044,847 (GRCm39) missense probably damaging 1.00
R8961:Cdh6 UTSW 15 13,041,447 (GRCm39) missense probably benign 0.12
R9218:Cdh6 UTSW 15 13,057,556 (GRCm39) missense probably null 0.37
R9258:Cdh6 UTSW 15 13,064,462 (GRCm39) missense probably damaging 1.00
R9511:Cdh6 UTSW 15 13,034,677 (GRCm39) missense probably damaging 1.00
R9608:Cdh6 UTSW 15 13,064,621 (GRCm39) missense probably damaging 1.00
R9636:Cdh6 UTSW 15 13,057,655 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- AGGCTGCAAAGACCTCTCAG -3'
(R):5'- TTGTTGTCTAAGGAGAATCAGTGAC -3'

Sequencing Primer
(F):5'- CCTTGGAGACTGATGAACTTCCAG -3'
(R):5'- GACTGACACAAAAATGCCTGTTTC -3'
Posted On 2015-04-17