Incidental Mutation 'R4429:Pcdh9'
ID 328345
Institutional Source Beutler Lab
Gene Symbol Pcdh9
Ensembl Gene ENSMUSG00000055421
Gene Name protocadherin 9
Synonyms C630029H24Rik, LOC382930, A730003J17Rik, 1500001L12Rik, C530050I23Rik
MMRRC Submission 041699-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.194) question?
Stock # R4429 (G1)
Quality Score 225
Status Not validated
Chromosome 14
Chromosomal Location 93250846-94128115 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 94124820 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Serine at position 327 (N327S)
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: N450S

PolyPhen 2 Score 0.319 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000070935
Gene: ENSMUSG00000055421
AA Change: N450S

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: N327S

PolyPhen 2 Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000142260
Gene: ENSMUSG00000055421
AA Change: N327S

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 possibly damaging
Transcript: ENSMUST00000193901
AA Change: N450S

PolyPhen 2 Score 0.800 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000141759
Gene: ENSMUSG00000055421
AA Change: N450S

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 possibly damaging
Transcript: ENSMUST00000194056
AA Change: N450S

PolyPhen 2 Score 0.572 (Sensitivity: 0.88; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000141602
Gene: ENSMUSG00000055421
AA Change: N450S

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 possibly damaging
Transcript: ENSMUST00000195376
AA Change: N450S

PolyPhen 2 Score 0.917 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000142224
Gene: ENSMUSG00000055421
AA Change: N450S

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: N450S

PolyPhen 2 Score 0.319 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000141396
Gene: ENSMUSG00000055421
AA Change: N450S

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
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.5%
Validation Efficiency
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: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
0610040J01Rik G T 5: 64,056,182 (GRCm39) probably benign Het
Abca5 T C 11: 110,202,236 (GRCm39) T390A probably benign Het
Ahcyl2 T G 6: 29,894,874 (GRCm39) V452G probably damaging Het
Ano4 T A 10: 88,828,804 (GRCm39) N545I probably damaging Het
Bag4 C T 8: 26,259,516 (GRCm39) A228T probably benign Het
Catip T A 1: 74,407,891 (GRCm39) probably benign Het
Chrna4 A G 2: 180,670,413 (GRCm39) S448P probably damaging Het
Cldn8 A C 16: 88,359,619 (GRCm39) M102R probably damaging Het
Cnpy3 T A 17: 47,058,070 (GRCm39) Q111L probably benign Het
Dnah8 A G 17: 30,971,120 (GRCm39) N2725D probably damaging Het
Dock8 T C 19: 25,042,754 (GRCm39) V112A probably benign Het
Ephb3 G A 16: 21,033,213 (GRCm39) E66K probably damaging Het
Gm6594 T A 17: 82,846,923 (GRCm39) D79E probably benign Het
Gtf2e2 T A 8: 34,242,521 (GRCm39) Y74* probably null Het
Hacd4 A T 4: 88,353,184 (GRCm39) F103I possibly damaging Het
Hap1 T C 11: 100,245,098 (GRCm39) T38A probably benign Het
Havcr2 T A 11: 46,347,387 (GRCm39) D72E probably damaging Het
Iqcg G A 16: 32,839,860 (GRCm39) T362I probably benign Het
Lect2 C T 13: 56,693,538 (GRCm39) probably null Het
Lemd3 T C 10: 120,813,893 (GRCm39) T447A probably benign Het
Lrrc72 T C 12: 36,258,623 (GRCm39) N78S probably damaging Het
Map3k14 A G 11: 103,118,410 (GRCm39) L592P probably damaging Het
Meioc T C 11: 102,566,546 (GRCm39) Y721H probably damaging Het
Mrps10 T A 17: 47,689,124 (GRCm39) probably null Het
Myo5c A G 9: 75,201,283 (GRCm39) Y1406C probably damaging Het
Myo7a T C 7: 97,702,395 (GRCm39) Y2098C probably damaging Het
Nol9 C T 4: 152,125,631 (GRCm39) T194I probably damaging Het
Nox3 G A 17: 3,733,233 (GRCm39) T206I probably benign Het
Nsd2 T G 5: 34,000,546 (GRCm39) M21R probably damaging Het
Pclo T G 5: 14,728,114 (GRCm39) probably benign Het
Pparg T A 6: 115,416,984 (GRCm39) M59K probably benign Het
Prag1 A G 8: 36,613,796 (GRCm39) K1116R probably damaging Het
Rhbdf1 C T 11: 32,163,369 (GRCm39) E368K probably benign Het
Rita1 A G 5: 120,747,626 (GRCm39) V224A probably damaging Het
Rsph6a T A 7: 18,807,988 (GRCm39) W384R probably damaging Het
Scn1a A T 2: 66,181,329 (GRCm39) Y65N possibly damaging Het
Serpina5 C A 12: 104,069,665 (GRCm39) F292L probably benign Het
Sf3b3 A C 8: 111,552,750 (GRCm39) L511V probably benign Het
Siglecg C T 7: 43,067,350 (GRCm39) P639L possibly damaging Het
Slc12a3 A T 8: 95,069,713 (GRCm39) I541F probably damaging Het
Slco6d1 T C 1: 98,424,091 (GRCm39) V581A possibly damaging Het
Sptbn2 T C 19: 4,788,383 (GRCm39) Y1121H probably damaging Het
Sytl5 A T X: 9,826,262 (GRCm39) N412Y probably damaging Het
Timm29 G C 9: 21,504,775 (GRCm39) A148P probably damaging Het
Tmem181a T A 17: 6,346,061 (GRCm39) L185H probably damaging Het
Tmem67 T A 4: 12,051,473 (GRCm39) N785I possibly damaging Het
Trhde A T 10: 114,339,028 (GRCm39) L594Q probably damaging Het
Uba6 C T 5: 86,268,406 (GRCm39) V941I probably damaging Het
Vmn1r174 T C 7: 23,453,565 (GRCm39) V77A probably benign Het
Zfp661 A G 2: 127,420,628 (GRCm39) V57A probably damaging Het
Zfp867 C T 11: 59,355,863 (GRCm39) D64N possibly damaging Het
Zp3r T C 1: 130,519,128 (GRCm39) T294A 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
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
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'- AAGGAGGCATTCGGTCCAAG -3'
(R):5'- CAAAGATTGCCCTCATTACAGTTTC -3'

Sequencing Primer
(F):5'- CGGTCCAAGCTGATAAACAATGTCTG -3'
(R):5'- GCCCTCATTACAGTTTCAGATAAGG -3'
Posted On 2015-07-07