Incidental Mutation 'R4621:Pcdh9'
ID 346182
Institutional Source Beutler Lab
Gene Symbol Pcdh9
Ensembl Gene ENSMUSG00000055421
Gene Name protocadherin 9
Synonyms C630029H24Rik, LOC382930, A730003J17Rik, 1500001L12Rik, C530050I23Rik
MMRRC Submission 041886-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.166) question?
Stock # R4621 (G1)
Quality Score 225
Status Validated
Chromosome 14
Chromosomal Location 93250846-94128115 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 94125079 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Valine at position 241 (I241V)
Ref Sequence ENSEMBL: ENSMUSP00000142260 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000068992] [ENSMUST00000192221] [ENSMUST00000193901] [ENSMUST00000194056] [ENSMUST00000195376] [ENSMUST00000195826]
AlphaFold F8VPK8
Predicted Effect probably benign
Transcript: ENSMUST00000068992
AA Change: I364V

PolyPhen 2 Score 0.038 (Sensitivity: 0.94; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000070935
Gene: ENSMUSG00000055421
AA Change: I364V

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 benign
Transcript: ENSMUST00000192221
AA Change: I241V

PolyPhen 2 Score 0.120 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000142260
Gene: ENSMUSG00000055421
AA Change: I241V

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 benign
Transcript: ENSMUST00000193901
AA Change: I364V

PolyPhen 2 Score 0.030 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000141759
Gene: ENSMUSG00000055421
AA Change: I364V

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 benign
Transcript: ENSMUST00000194056
AA Change: I364V

PolyPhen 2 Score 0.022 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000141602
Gene: ENSMUSG00000055421
AA Change: I364V

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: I364V

PolyPhen 2 Score 0.061 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000142224
Gene: ENSMUSG00000055421
AA Change: I364V

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 benign
Transcript: ENSMUST00000195826
AA Change: I364V

PolyPhen 2 Score 0.038 (Sensitivity: 0.94; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000141396
Gene: ENSMUSG00000055421
AA Change: I364V

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 0.0705 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.9%
Validation Efficiency 100% (90/90)
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: 77 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abhd2 T C 7: 78,975,235 (GRCm39) Y142H probably damaging Het
Abra C T 15: 41,732,620 (GRCm39) D149N probably benign Het
Acin1 A T 14: 54,890,900 (GRCm39) probably benign Het
Adap2 T A 11: 80,064,899 (GRCm39) probably null Het
Afdn A G 17: 14,109,082 (GRCm39) E1535G probably damaging Het
Ajm1 G A 2: 25,468,412 (GRCm39) P500S probably damaging Het
Ak9 A G 10: 41,282,887 (GRCm39) N1218D possibly damaging Het
Angptl1 G A 1: 156,672,494 (GRCm39) V107M probably damaging Het
Arhgap26 G A 18: 39,032,894 (GRCm39) probably benign Het
Cage1 A C 13: 38,209,477 (GRCm39) S61A possibly damaging Het
Cdadc1 T C 14: 59,824,004 (GRCm39) T163A probably benign Het
Celsr2 A T 3: 108,302,532 (GRCm39) V2568D possibly damaging Het
Cep44 G A 8: 56,995,951 (GRCm39) T166M probably damaging Het
Cnksr3 T C 10: 7,076,182 (GRCm39) K187E possibly damaging Het
Cyp20a1 A G 1: 60,415,258 (GRCm39) T295A probably benign Het
Dus2 T A 8: 106,757,074 (GRCm39) M88K probably damaging Het
E330034G19Rik A T 14: 24,346,070 (GRCm39) probably benign Het
Ecrg4 G A 1: 43,776,412 (GRCm39) probably null Het
Efna5 T C 17: 62,958,040 (GRCm39) D72G probably benign Het
Epb41l2 T C 10: 25,378,038 (GRCm39) probably null Het
Espn A G 4: 152,215,709 (GRCm39) S408P probably damaging Het
Evi5l T C 8: 4,252,909 (GRCm39) probably benign Het
F830016B08Rik G A 18: 60,433,939 (GRCm39) V341I probably benign Het
Flii A G 11: 60,606,937 (GRCm39) L1013P possibly damaging Het
Fndc10 G A 4: 155,779,264 (GRCm39) V103M probably damaging Het
Frem3 T A 8: 81,395,820 (GRCm39) probably null Het
Gltp C T 5: 114,812,188 (GRCm39) R106Q probably damaging Het
Gtf3c3 A G 1: 54,458,575 (GRCm39) Y449H probably damaging Het
H1f9 G A 11: 94,858,986 (GRCm39) V94M probably damaging Het
Hmga1b T C 11: 120,653,866 (GRCm39) V51A probably damaging Het
Hsph1 A G 5: 149,542,308 (GRCm39) V705A probably benign Het
Igkv13-84 T C 6: 68,916,783 (GRCm39) S27P possibly damaging Het
Il15ra A G 2: 11,723,140 (GRCm39) N55D possibly damaging Het
Kctd19 T G 8: 106,123,103 (GRCm39) N104H probably damaging Het
Kif27 T G 13: 58,478,827 (GRCm39) D572A probably benign Het
Larp1b G A 3: 40,918,424 (GRCm39) G22R possibly damaging Het
Lcn2 A T 2: 32,274,655 (GRCm39) probably benign Het
Lmtk2 T A 5: 144,111,752 (GRCm39) I824N probably benign Het
Ltbp2 A G 12: 84,856,122 (GRCm39) I707T probably damaging Het
Macf1 A G 4: 123,266,141 (GRCm39) probably null Het
Magel2 A T 7: 62,027,486 (GRCm39) H130L unknown Het
Mcoln1 A G 8: 3,555,923 (GRCm39) I73V probably damaging Het
Mplkipl1 C T 19: 61,164,364 (GRCm39) G24R unknown Het
Mycbp2 G T 14: 103,457,415 (GRCm39) T1627K probably benign Het
Myh8 A G 11: 67,177,084 (GRCm39) E412G probably damaging Het
Myo9a T A 9: 59,778,355 (GRCm39) D1370E probably benign Het
Ndufaf5 A G 2: 140,025,845 (GRCm39) T135A probably benign Het
Neb G A 2: 52,161,051 (GRCm39) Q2207* probably null Het
Nek3 T C 8: 22,647,055 (GRCm39) Y160C probably damaging Het
Or2y6 G C 11: 52,104,706 (GRCm39) L37V probably benign Het
Or5k8 A T 16: 58,644,469 (GRCm39) I201N possibly damaging Het
Osbpl8 A G 10: 111,105,279 (GRCm39) I245V probably benign Het
Pcdhb12 A G 18: 37,570,213 (GRCm39) Q453R probably benign Het
Pcdhb2 A G 18: 37,428,980 (GRCm39) T318A probably benign Het
Prlr T A 15: 10,319,462 (GRCm39) probably benign Het
Ptprz1 C T 6: 23,001,453 (GRCm39) A1181V possibly damaging Het
Racgap1 C A 15: 99,524,087 (GRCm39) S440I probably benign Het
Rap1gap2 A G 11: 74,326,525 (GRCm39) probably null Het
Rbm5 A G 9: 107,631,345 (GRCm39) V244A probably damaging Het
Rexo5 T G 7: 119,418,722 (GRCm39) I254R probably benign Het
Robo2 A T 16: 73,782,821 (GRCm39) S316T probably benign Het
Satb2 A T 1: 56,884,778 (GRCm39) V382E probably damaging Het
Scg2 C T 1: 79,414,381 (GRCm39) R114Q probably benign Het
Scube2 T C 7: 109,399,857 (GRCm39) D893G possibly damaging Het
Snrpn T C 7: 59,637,274 (GRCm39) D14G possibly damaging Het
Spag17 A G 3: 100,010,559 (GRCm39) T2018A probably benign Het
Spata9 T G 13: 76,116,001 (GRCm39) F17V possibly damaging Het
Supt6 A G 11: 78,103,572 (GRCm39) Y1378H possibly damaging Het
Thsd7b T C 1: 129,358,652 (GRCm39) S29P possibly damaging Het
Tmem59 A T 4: 107,047,915 (GRCm39) probably benign Het
Tmem87a A G 2: 120,227,905 (GRCm39) S81P probably benign Het
Togaram1 A T 12: 65,029,224 (GRCm39) E882D possibly damaging Het
Trbj2-4 T A 6: 41,520,308 (GRCm39) probably benign Het
Trim42 T A 9: 97,245,201 (GRCm39) Y533F probably benign Het
Tssk5 C T 15: 76,256,668 (GRCm39) R280Q probably benign Het
Vmn1r82 A G 7: 12,039,263 (GRCm39) T179A possibly damaging Het
Yipf7 T A 5: 69,676,704 (GRCm39) Q145L possibly damaging 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
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
R5753:Pcdh9 UTSW 14 94,125,597 (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'- CCCTCATAGTCCAGCAGAGAAG -3'
(R):5'- TGCAACCAAAAGACTCTTTGC -3'

Sequencing Primer
(F):5'- AAGAGGTCTCTAGCAGATACTGGTTG -3'
(R):5'- TGCTTTAAATAATACAACTGGGCTG -3'
Posted On 2015-09-25