Incidental Mutation 'PIT4651001:Cdh6'
ID 556699
Institutional Source Beutler Lab
Gene Symbol Cdh6
Ensembl Gene ENSMUSG00000039385
Gene Name cadherin 6
Synonyms K-cadherin, cad6
Accession Numbers
Essential gene? Probably non essential (E-score: 0.204) question?
Stock # PIT4651001 (G1)
Quality Score 225.009
Status Not validated
Chromosome 15
Chromosomal Location 13028787-13173761 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 13044805 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Leucine at position 439 (S439L)
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 possibly damaging
Transcript: ENSMUST00000036439
AA Change: S439L

PolyPhen 2 Score 0.690 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000037113
Gene: ENSMUSG00000039385
AA Change: S439L

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
Coding Region Coverage
  • 1x: 93.1%
  • 3x: 90.7%
  • 10x: 84.4%
  • 20x: 70.4%
Validation Efficiency
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: 74 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2210408I21Rik A T 13: 77,408,014 (GRCm39) I428L probably benign Het
Aass T C 6: 23,118,750 (GRCm39) I131V probably benign Het
Alcam T A 16: 52,115,550 (GRCm39) K189N probably benign Het
Ankrd50 C A 3: 38,509,959 (GRCm39) E803* probably null Het
Ankrd53 A G 6: 83,742,715 (GRCm39) D236G probably damaging Het
Bard1 A G 1: 71,114,087 (GRCm39) V298A probably benign Het
Cacna1d C T 14: 29,900,602 (GRCm39) G361D probably damaging Het
Camkk1 A G 11: 72,916,647 (GRCm39) S82G probably benign Het
Ccr4 A T 9: 114,321,261 (GRCm39) V268E probably benign Het
Ces1e G T 8: 93,941,711 (GRCm39) A254E probably benign Het
Cfap46 T C 7: 139,225,467 (GRCm39) T1078A Het
Cyp46a1 A G 12: 108,319,367 (GRCm39) D288G probably benign Het
Dnah6 T C 6: 73,037,243 (GRCm39) N3333S probably benign Het
Dzip3 A G 16: 48,765,241 (GRCm39) V491A probably benign Het
Egr1 G T 18: 34,996,240 (GRCm39) E341* probably null Het
Enpp1 G A 10: 24,529,848 (GRCm39) P597S probably benign Het
Ercc3 A T 18: 32,373,365 (GRCm39) probably benign Het
Fbn1 T C 2: 125,205,909 (GRCm39) probably null Het
Fbxw11 T C 11: 32,661,999 (GRCm39) probably null Het
Fhip1a C T 3: 85,590,948 (GRCm39) A389T probably damaging Het
Gbf1 A G 19: 46,151,982 (GRCm39) N5S probably benign Het
Gbp4 T A 5: 105,266,289 (GRCm39) H584L probably benign Het
Gcgr G T 11: 120,428,968 (GRCm39) C402F probably damaging Het
Grm7 T A 6: 110,623,050 (GRCm39) N74K probably benign Het
H1f9 A G 11: 94,859,142 (GRCm39) S146G probably benign Het
Hoxa10 T G 6: 52,211,877 (GRCm39) N13T possibly damaging Het
Ice1 A T 13: 70,772,040 (GRCm39) probably null Het
Il22 C A 10: 118,041,495 (GRCm39) N69K probably damaging Het
Il9r A T 11: 32,141,798 (GRCm39) H319Q probably benign Het
Itgax A G 7: 127,748,282 (GRCm39) T1104A probably benign Het
Jag1 C T 2: 136,943,617 (GRCm39) G193D probably damaging Het
Krt13 T A 11: 100,010,862 (GRCm39) D164V probably damaging Het
Lepr T C 4: 101,649,194 (GRCm39) M865T probably damaging Het
Lmf2 G A 15: 89,236,272 (GRCm39) H576Y possibly damaging Het
Lrrc8c C T 5: 105,756,189 (GRCm39) H655Y probably benign Het
Mapk6 A T 9: 75,304,869 (GRCm39) S183T possibly damaging Het
Mcrs1 A T 15: 99,144,832 (GRCm39) Y261N probably damaging Het
Mon1b G A 8: 114,365,254 (GRCm39) G194D probably benign Het
Myo18b C T 5: 112,982,301 (GRCm39) R1144Q probably benign Het
Myo9b T A 8: 71,795,456 (GRCm39) H808Q possibly damaging Het
Ngdn T C 14: 55,253,657 (GRCm39) I15T probably benign Het
Nhsl1 T G 10: 18,284,183 (GRCm39) S41R probably damaging Het
Numa1 A T 7: 101,663,141 (GRCm39) K2089M probably damaging Het
Obi1 T A 14: 104,743,692 (GRCm39) D129V probably damaging Het
Obscn A G 11: 58,932,507 (GRCm39) L4900P probably damaging Het
Olfm4 T A 14: 80,258,925 (GRCm39) L391Q probably benign Het
Or10g9b A T 9: 39,917,526 (GRCm39) C240S probably damaging Het
Or2ag1 A G 7: 106,472,730 (GRCm39) C241R probably damaging Het
Or5b106 T A 19: 13,123,991 (GRCm39) I11F probably benign Het
Or5b111 A G 19: 13,291,556 (GRCm39) I31T probably benign Het
Or5m9 T C 2: 85,876,862 (GRCm39) L12P probably damaging Het
Parn T A 16: 13,449,431 (GRCm39) N302Y probably benign Het
Pi4k2b T G 5: 52,905,812 (GRCm39) S118A possibly damaging Het
Piwil4 C T 9: 14,620,195 (GRCm39) V704I possibly damaging Het
Pm20d2 G A 4: 33,181,715 (GRCm39) T296M probably damaging Het
Pmpcb C T 5: 21,951,048 (GRCm39) A270V probably benign Het
Pnpt1 T C 11: 29,106,945 (GRCm39) probably null Het
Prkn T A 17: 11,286,130 (GRCm39) L41Q probably damaging Het
Rc3h1 C A 1: 160,791,110 (GRCm39) N931K probably benign Het
Rlf A G 4: 121,007,510 (GRCm39) V600A probably damaging Het
Rpl27rt A T 18: 34,870,892 (GRCm39) Q142L unknown Het
Sall1 T G 8: 89,757,731 (GRCm39) Q791P probably damaging Het
Sema3c T A 5: 17,899,731 (GRCm39) Y408N probably benign Het
Serpinb13 C T 1: 106,910,574 (GRCm39) S66L probably damaging Het
Tmem181a A T 17: 6,351,170 (GRCm39) M319L probably benign Het
Trim24 T C 6: 37,877,667 (GRCm39) probably null Het
Ttn T A 2: 76,719,278 (GRCm39) T7234S unknown Het
Unc13c T A 9: 73,391,021 (GRCm39) M2076L possibly damaging Het
Uroc1 C T 6: 90,340,095 (GRCm39) R667* probably null Het
Uvrag A G 7: 98,555,727 (GRCm39) F456L probably benign Het
Vmn1r215 T C 13: 23,260,530 (GRCm39) V190A probably damaging Het
Vmn2r50 T A 7: 9,771,659 (GRCm39) T681S probably benign Het
Vmn2r65 T A 7: 84,595,461 (GRCm39) T408S probably benign Het
Vps33b A G 7: 79,939,755 (GRCm39) D502G probably damaging 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
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
R3903:Cdh6 UTSW 15 13,042,661 (GRCm39) missense probably benign 0.39
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'- TGGCTCTACACAGTCCCTTG -3'
(R):5'- CTTAACGTTGCAGTTACAGATGC -3'

Sequencing Primer
(F):5'- TGGGAAAGCATATCTACCATGTACG -3'
(R):5'- CGTTGCAGTTACAGATGCTTCAAAG -3'
Posted On 2019-06-07