Incidental Mutation 'R5753:Pcdh9'
ID 444911
Institutional Source Beutler Lab
Gene Symbol Pcdh9
Ensembl Gene ENSMUSG00000055421
Gene Name protocadherin 9
Synonyms C630029H24Rik, LOC382930, A730003J17Rik, 1500001L12Rik, C530050I23Rik
MMRRC Submission 043358-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.166) question?
Stock # R5753 (G1)
Quality Score 225
Status Validated
Chromosome 14
Chromosomal Location 93250846-94128115 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 94125597 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Valine at position 191 (D191V)
Ref Sequence ENSEMBL: ENSMUSP00000141759 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000068992] [ENSMUST00000192221] [ENSMUST00000193901] [ENSMUST00000194056] [ENSMUST00000195376] [ENSMUST00000195826]
AlphaFold F8VPK8
Predicted Effect probably damaging
Transcript: ENSMUST00000068992
AA Change: D191V

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000070935
Gene: ENSMUSG00000055421
AA Change: D191V

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
CA 49 140 8.37e-3 SMART
CA 164 250 1.01e-20 SMART
CA 274 356 2.34e-25 SMART
CA 386 467 2.14e-19 SMART
CA 491 570 4.27e-28 SMART
CA 594 673 2.45e-28 SMART
CA 700 782 1.01e-6 SMART
transmembrane domain 814 836 N/A INTRINSIC
low complexity region 858 883 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000192221
AA Change: D68V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000142260
Gene: ENSMUSG00000055421
AA Change: D68V

DomainStartEndE-ValueType
CA 41 127 1.01e-20 SMART
CA 151 233 2.34e-25 SMART
CA 263 344 2.14e-19 SMART
CA 368 447 4.27e-28 SMART
CA 471 550 2.45e-28 SMART
CA 577 659 1.01e-6 SMART
transmembrane domain 691 713 N/A INTRINSIC
low complexity region 735 760 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000192817
Predicted Effect probably damaging
Transcript: ENSMUST00000193901
AA Change: D191V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000141759
Gene: ENSMUSG00000055421
AA Change: D191V

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
CA 49 140 8.37e-3 SMART
CA 164 250 1.01e-20 SMART
CA 274 356 2.34e-25 SMART
CA 386 467 2.14e-19 SMART
CA 491 570 4.27e-28 SMART
CA 594 673 2.45e-28 SMART
CA 700 782 1.01e-6 SMART
transmembrane domain 814 836 N/A INTRINSIC
low complexity region 858 883 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000194056
AA Change: D191V

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000141602
Gene: ENSMUSG00000055421
AA Change: D191V

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
CA 49 140 4.1e-5 SMART
CA 164 250 4.8e-23 SMART
CA 274 356 1.2e-27 SMART
CA 386 467 1.1e-21 SMART
CA 491 570 2e-30 SMART
CA 594 673 1.2e-30 SMART
CA 700 782 4.9e-9 SMART
transmembrane domain 814 836 N/A INTRINSIC
low complexity region 860 873 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000194129
Predicted Effect probably benign
Transcript: ENSMUST00000195376
AA Change: D191V

PolyPhen 2 Score 0.109 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000142224
Gene: ENSMUSG00000055421
AA Change: D191V

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
CA 49 140 4.1e-5 SMART
CA 164 250 4.8e-23 SMART
CA 274 356 1.2e-27 SMART
CA 386 467 1.1e-21 SMART
CA 491 570 2e-30 SMART
CA 594 673 1.2e-30 SMART
CA 700 782 4.9e-9 SMART
transmembrane domain 814 836 N/A INTRINSIC
low complexity region 858 883 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000195826
AA Change: D191V

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000141396
Gene: ENSMUSG00000055421
AA Change: D191V

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
CA 49 140 8.37e-3 SMART
CA 164 250 1.01e-20 SMART
CA 274 356 2.34e-25 SMART
CA 386 467 2.14e-19 SMART
CA 491 570 4.27e-28 SMART
CA 594 673 2.45e-28 SMART
CA 700 782 1.01e-6 SMART
transmembrane domain 814 836 N/A INTRINSIC
low complexity region 858 883 N/A INTRINSIC
Meta Mutation Damage Score 0.5885 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 96.0%
Validation Efficiency 97% (58/60)
MGI Phenotype FUNCTION: This gene encodes a member of the protocadherin family, and cadherin superfamily, of transmembrane proteins containing cadherin domains. These proteins mediate cell adhesion in neural tissues in the presence of calcium. The encoded protein may be involved in signaling at neuronal synaptic junctions. Sharing a characteristic with other protocadherin genes, this gene has a notably large exon that encodes multiple cadherin domains and a transmembrane region. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2012]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit impaired long-term social and bject recognition and sensorimotor development. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2310003L06Rik C T 5: 88,120,374 (GRCm39) T377I probably damaging Het
Abcb1a A G 5: 8,773,160 (GRCm39) D796G probably damaging Het
Actn3 T C 19: 4,914,595 (GRCm39) probably null Het
Ada A T 2: 163,577,318 (GRCm39) S57T probably benign Het
Adamts6 A G 13: 104,483,858 (GRCm39) Y359C probably damaging Het
Adcy1 A T 11: 7,080,300 (GRCm39) I348F probably damaging Het
Ankrd11 T C 8: 123,622,043 (GRCm39) E603G possibly damaging Het
Bcas3 A G 11: 85,712,910 (GRCm39) probably benign Het
Cldn1 C A 16: 26,181,871 (GRCm39) V113L probably benign Het
Dock9 T C 14: 121,872,037 (GRCm39) T540A probably benign Het
Erp27 A G 6: 136,896,875 (GRCm39) F109S probably damaging Het
F13a1 G A 13: 37,082,082 (GRCm39) Q541* probably null Het
Fam124a T C 14: 62,843,988 (GRCm39) S499P probably benign Het
Fgd3 T A 13: 49,428,416 (GRCm39) E486V possibly damaging Het
Flnc T C 6: 29,433,488 (GRCm39) S11P probably benign Het
Gm12508 C A 4: 55,254,787 (GRCm39) noncoding transcript Het
Grk2 C T 19: 4,340,496 (GRCm39) R295H probably damaging Het
Gtf2ird1 A G 5: 134,439,837 (GRCm39) M131T probably damaging Het
H4c4 G A 13: 23,765,587 (GRCm39) M1I probably null Het
Itpripl2 A G 7: 118,090,232 (GRCm39) V109A probably damaging Het
Jakmip2 T C 18: 43,692,181 (GRCm39) E585G probably damaging Het
Kbtbd3 A T 9: 4,331,404 (GRCm39) I593F possibly damaging Het
Lgr4 C T 2: 109,832,857 (GRCm39) Q316* probably null Het
Mcf2l T C 8: 13,049,993 (GRCm39) F305S probably damaging Het
Nos1ap T A 1: 170,176,968 (GRCm39) K145M probably damaging Het
Or4c3 T C 2: 89,851,847 (GRCm39) T188A possibly damaging Het
Or4k51 T A 2: 111,585,146 (GRCm39) I184K possibly damaging Het
Or4q3 T A 14: 50,583,045 (GRCm39) T285S probably damaging Het
Or51b17 A G 7: 103,542,408 (GRCm39) L178P probably damaging Het
Or5d18 G A 2: 87,864,920 (GRCm39) L188F probably damaging Het
Or5w18 A T 2: 87,633,596 (GRCm39) M288L probably benign Het
Or7a40 A T 16: 16,491,484 (GRCm39) Y120* probably null Het
Pde4d T A 13: 109,909,256 (GRCm39) probably benign Het
Phkb C T 8: 86,604,859 (GRCm39) A88V probably damaging Het
Plec A G 15: 76,057,620 (GRCm39) S4128P probably damaging Het
Plekha5 A T 6: 140,482,730 (GRCm39) probably null Het
Rgs13 A C 1: 144,016,478 (GRCm39) N88K probably benign Het
Rho T A 6: 115,912,448 (GRCm39) I104N probably damaging Het
Rnps1 T C 17: 24,637,138 (GRCm39) probably benign Het
Saxo5 A T 8: 3,534,112 (GRCm39) I350L probably benign Het
Slc10a7 G T 8: 79,251,928 (GRCm39) probably null Het
Slc39a7 C T 17: 34,249,150 (GRCm39) R246K probably damaging Het
Sort1 G C 3: 108,253,090 (GRCm39) G510A probably damaging Het
Spag6l A G 16: 16,584,831 (GRCm39) probably null Het
Sync T A 4: 129,187,179 (GRCm39) Y70* probably null Het
Timm8a2 T C 14: 122,272,289 (GRCm39) V64A probably benign Het
Tnfrsf11b C A 15: 54,117,455 (GRCm39) V267L possibly damaging Het
Trim30b A G 7: 104,006,544 (GRCm39) V104A possibly damaging Het
Tusc3 T C 8: 39,564,100 (GRCm39) S244P probably damaging Het
Usp16 T A 16: 87,279,787 (GRCm39) Y746N probably damaging Het
Vax1 G T 19: 59,154,814 (GRCm39) H274Q probably benign Het
Vmn2r108 A G 17: 20,683,179 (GRCm39) V675A probably damaging Het
Vmn2r12 A T 5: 109,239,670 (GRCm39) W298R probably damaging Het
Zfp948 A G 17: 21,807,156 (GRCm39) N116S probably damaging Het
Zkscan2 A G 7: 123,079,923 (GRCm39) V678A probably benign Het
Other mutations in Pcdh9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00482:Pcdh9 APN 14 93,564,130 (GRCm39) missense probably damaging 1.00
IGL02183:Pcdh9 APN 14 94,123,720 (GRCm39) missense probably benign 0.01
IGL02244:Pcdh9 APN 14 93,564,204 (GRCm39) missense probably damaging 1.00
IGL02571:Pcdh9 APN 14 93,798,023 (GRCm39) splice site probably benign
IGL03018:Pcdh9 APN 14 93,253,012 (GRCm39) missense probably null
I1329:Pcdh9 UTSW 14 94,123,645 (GRCm39) missense probably benign 0.00
R0027:Pcdh9 UTSW 14 94,126,081 (GRCm39) missense probably null 0.99
R0027:Pcdh9 UTSW 14 94,126,081 (GRCm39) missense probably null 0.99
R0477:Pcdh9 UTSW 14 94,125,114 (GRCm39) missense probably damaging 0.99
R0499:Pcdh9 UTSW 14 94,123,671 (GRCm39) missense probably damaging 1.00
R0787:Pcdh9 UTSW 14 94,124,193 (GRCm39) missense possibly damaging 0.88
R1205:Pcdh9 UTSW 14 94,123,501 (GRCm39) missense probably benign 0.01
R1616:Pcdh9 UTSW 14 94,124,405 (GRCm39) nonsense probably null
R1620:Pcdh9 UTSW 14 94,125,741 (GRCm39) missense probably damaging 1.00
R1622:Pcdh9 UTSW 14 94,123,311 (GRCm39) missense probably benign 0.03
R1708:Pcdh9 UTSW 14 94,125,741 (GRCm39) missense probably damaging 1.00
R1721:Pcdh9 UTSW 14 94,125,471 (GRCm39) missense probably damaging 1.00
R1753:Pcdh9 UTSW 14 94,124,661 (GRCm39) missense probably benign 0.33
R1799:Pcdh9 UTSW 14 94,126,107 (GRCm39) missense probably benign 0.36
R1867:Pcdh9 UTSW 14 94,125,471 (GRCm39) missense probably damaging 1.00
R1987:Pcdh9 UTSW 14 94,125,741 (GRCm39) missense probably damaging 1.00
R1988:Pcdh9 UTSW 14 94,125,741 (GRCm39) missense probably damaging 1.00
R2444:Pcdh9 UTSW 14 94,124,227 (GRCm39) missense probably benign 0.10
R3895:Pcdh9 UTSW 14 94,124,974 (GRCm39) missense probably damaging 1.00
R3926:Pcdh9 UTSW 14 94,124,246 (GRCm39) nonsense probably null
R4166:Pcdh9 UTSW 14 94,124,956 (GRCm39) nonsense probably null
R4429:Pcdh9 UTSW 14 94,124,820 (GRCm39) missense probably damaging 0.96
R4589:Pcdh9 UTSW 14 94,125,628 (GRCm39) missense probably damaging 1.00
R4604:Pcdh9 UTSW 14 94,124,616 (GRCm39) missense probably damaging 1.00
R4607:Pcdh9 UTSW 14 93,253,009 (GRCm39) missense probably benign 0.08
R4621:Pcdh9 UTSW 14 94,125,079 (GRCm39) missense probably benign 0.12
R4624:Pcdh9 UTSW 14 94,123,845 (GRCm39) missense probably damaging 1.00
R4712:Pcdh9 UTSW 14 94,126,067 (GRCm39) missense probably damaging 1.00
R4788:Pcdh9 UTSW 14 94,124,851 (GRCm39) missense probably damaging 1.00
R4831:Pcdh9 UTSW 14 94,125,377 (GRCm39) missense probably damaging 1.00
R4883:Pcdh9 UTSW 14 94,126,164 (GRCm39) missense possibly damaging 0.83
R5034:Pcdh9 UTSW 14 93,564,285 (GRCm39) missense probably benign 0.13
R5175:Pcdh9 UTSW 14 94,125,879 (GRCm39) missense probably damaging 1.00
R5637:Pcdh9 UTSW 14 94,123,198 (GRCm39) missense possibly damaging 0.91
R5743:Pcdh9 UTSW 14 94,124,160 (GRCm39) missense probably damaging 1.00
R5770:Pcdh9 UTSW 14 94,124,379 (GRCm39) missense probably damaging 1.00
R5900:Pcdh9 UTSW 14 93,564,156 (GRCm39) missense probably damaging 0.98
R5986:Pcdh9 UTSW 14 94,124,484 (GRCm39) missense probably damaging 1.00
R6052:Pcdh9 UTSW 14 94,123,282 (GRCm39) missense probably benign 0.40
R6113:Pcdh9 UTSW 14 94,124,544 (GRCm39) missense probably damaging 1.00
R6223:Pcdh9 UTSW 14 93,253,169 (GRCm39) missense probably benign 0.18
R6415:Pcdh9 UTSW 14 93,253,278 (GRCm39) missense possibly damaging 0.83
R6435:Pcdh9 UTSW 14 94,125,280 (GRCm39) missense probably benign 0.01
R7064:Pcdh9 UTSW 14 94,123,585 (GRCm39) missense probably damaging 1.00
R7143:Pcdh9 UTSW 14 94,125,708 (GRCm39) missense probably damaging 0.99
R7219:Pcdh9 UTSW 14 93,253,216 (GRCm39) missense possibly damaging 0.87
R7262:Pcdh9 UTSW 14 93,253,141 (GRCm39) missense probably benign 0.01
R7354:Pcdh9 UTSW 14 94,125,706 (GRCm39) missense probably benign 0.28
R7369:Pcdh9 UTSW 14 94,123,803 (GRCm39) missense possibly damaging 0.67
R7427:Pcdh9 UTSW 14 94,124,547 (GRCm39) missense probably damaging 1.00
R7428:Pcdh9 UTSW 14 94,124,547 (GRCm39) missense probably damaging 1.00
R7780:Pcdh9 UTSW 14 94,123,987 (GRCm39) missense possibly damaging 0.91
R7870:Pcdh9 UTSW 14 94,124,693 (GRCm39) missense probably damaging 0.97
R7921:Pcdh9 UTSW 14 93,253,001 (GRCm39) missense probably benign
R8052:Pcdh9 UTSW 14 94,123,222 (GRCm39) missense probably benign 0.00
R8252:Pcdh9 UTSW 14 94,126,086 (GRCm39) missense probably damaging 1.00
R8671:Pcdh9 UTSW 14 94,126,086 (GRCm39) missense probably damaging 1.00
R8672:Pcdh9 UTSW 14 94,124,529 (GRCm39) missense probably benign 0.08
R8724:Pcdh9 UTSW 14 94,124,583 (GRCm39) missense probably benign 0.19
R8974:Pcdh9 UTSW 14 94,125,113 (GRCm39) missense probably benign 0.20
R9044:Pcdh9 UTSW 14 94,124,247 (GRCm39) missense probably damaging 1.00
R9486:Pcdh9 UTSW 14 93,797,956 (GRCm39) missense possibly damaging 0.73
R9534:Pcdh9 UTSW 14 94,123,656 (GRCm39) missense probably damaging 0.99
X0012:Pcdh9 UTSW 14 94,124,080 (GRCm39) missense possibly damaging 0.71
X0067:Pcdh9 UTSW 14 93,564,285 (GRCm39) missense probably benign 0.13
Predicted Primers PCR Primer
(F):5'- GGCCTGTTGTCATTGACATC -3'
(R):5'- AGTAGTGATCCTCCCCAATGAC -3'

Sequencing Primer
(F):5'- GTTGTCATTGACATCACTTACTGTG -3'
(R):5'- CCAATGACTTTTTCAGGCTGATC -3'
Posted On 2016-11-21