Incidental Mutation 'R8252:Pcdh9'
ID 640204
Institutional Source Beutler Lab
Gene Symbol Pcdh9
Ensembl Gene ENSMUSG00000055421
Gene Name protocadherin 9
Synonyms C630029H24Rik, LOC382930, A730003J17Rik, 1500001L12Rik, C530050I23Rik
MMRRC Submission 067678-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.194) question?
Stock # R8252 (G1)
Quality Score 225.009
Status Validated
Chromosome 14
Chromosomal Location 93250846-94128115 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 94126086 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 28 (Y28C)
Ref Sequence ENSEMBL: ENSMUSP00000070935 (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: Y28C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000070935
Gene: ENSMUSG00000055421
AA Change: Y28C

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
SMART Domains Protein: ENSMUSP00000142260
Gene: ENSMUSG00000055421

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 probably damaging
Transcript: ENSMUST00000193901
AA Change: Y28C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000141759
Gene: ENSMUSG00000055421
AA Change: Y28C

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: Y28C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000141602
Gene: ENSMUSG00000055421
AA Change: Y28C

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 damaging
Transcript: ENSMUST00000195376
AA Change: Y28C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000142224
Gene: ENSMUSG00000055421
AA Change: Y28C

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: Y28C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000141396
Gene: ENSMUSG00000055421
AA Change: Y28C

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: 99.9%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.7%
Validation Efficiency 100% (60/60)
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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abi1 T C 2: 22,861,284 (GRCm39) probably benign Het
Ano4 A G 10: 88,816,881 (GRCm39) I644T probably damaging Het
Arhgap18 T A 10: 26,730,932 (GRCm39) D203E probably benign Het
Ascc3 T A 10: 50,518,706 (GRCm39) M337K probably benign Het
Atg13 G C 2: 91,510,699 (GRCm39) P343A probably benign Het
Cacna1c C T 6: 118,634,335 (GRCm39) V1058I Het
Cd180 A G 13: 102,842,504 (GRCm39) T517A probably benign Het
Cd1d2 A C 3: 86,894,375 (GRCm39) I48L probably benign Het
Cdh19 C T 1: 110,817,615 (GRCm39) C709Y probably benign Het
Chst10 T C 1: 38,923,433 (GRCm39) D51G probably benign Het
Clec2g G A 6: 128,958,335 (GRCm39) E184K probably benign Het
Col19a1 T A 1: 24,319,048 (GRCm39) H1014L probably benign Het
Fam135b T A 15: 71,404,872 (GRCm39) H58L probably benign Het
Fam171b A G 2: 83,708,586 (GRCm39) I363V probably benign Het
Hecw1 C A 13: 14,515,425 (GRCm39) G236W probably damaging Het
Htra3 A G 5: 35,810,305 (GRCm39) M459T probably benign Het
Iglc2 A T 16: 19,017,520 (GRCm39) C27* probably null Het
Il36b A T 2: 24,048,825 (GRCm39) T77S possibly damaging Het
Kif1b A T 4: 149,358,262 (GRCm39) N135K probably damaging Het
Krt5 A T 15: 101,620,794 (GRCm39) I151N probably damaging Het
Lama4 A T 10: 38,936,142 (GRCm39) M606L probably benign Het
Lgr6 T A 1: 134,931,215 (GRCm39) S280C probably null Het
Msh3 T A 13: 92,357,569 (GRCm39) T967S probably damaging Het
Ndufb4 T C 16: 37,474,637 (GRCm39) T29A probably benign Het
Nfe2l1 T C 11: 96,710,058 (GRCm39) M724V probably benign Het
Nudt12 T C 17: 59,318,089 (GRCm39) Y52C probably damaging Het
Nutm1 G T 2: 112,082,174 (GRCm39) Q301K probably damaging Het
Or2t46 T A 11: 58,471,958 (GRCm39) I96N probably damaging Het
Or4c102 A G 2: 88,423,011 (GRCm39) R288G probably damaging Het
Or5p50 A G 7: 107,421,776 (GRCm39) I300T probably damaging Het
Or6e1 T A 14: 54,519,704 (GRCm39) Y216F possibly damaging Het
Pcdha11 G C 18: 37,140,590 (GRCm39) V740L possibly damaging Het
Pkd1l2 T C 8: 117,767,472 (GRCm39) T1273A probably benign Het
Pla2g4a T C 1: 149,727,058 (GRCm39) D574G probably damaging Het
Prrc2b A T 2: 32,109,392 (GRCm39) Q1719L possibly damaging Het
Psap A G 10: 60,113,511 (GRCm39) probably benign Het
Pwwp3a A G 10: 80,077,694 (GRCm39) I656V probably benign Het
Rab11fip2 C T 19: 59,925,422 (GRCm39) S265N probably benign Het
Rnf10 A T 5: 115,398,373 (GRCm39) D53E probably benign Het
Scgb2b11 T C 7: 31,908,764 (GRCm39) E112G probably benign Het
Scml4 T C 10: 42,800,100 (GRCm39) Y85H noncoding transcript Het
Setd5 T A 6: 113,127,916 (GRCm39) Y1290N probably benign Het
Sgk1 T A 10: 21,873,298 (GRCm39) C375S probably damaging Het
Sik2 A G 9: 50,828,415 (GRCm39) V209A possibly damaging Het
Sipa1l2 A T 8: 126,195,410 (GRCm39) V776D probably damaging Het
Slamf1 T A 1: 171,594,796 (GRCm39) M1K probably null Het
Slc26a7 T C 4: 14,621,415 (GRCm39) probably benign Het
Spg11 G T 2: 121,918,820 (GRCm39) probably benign Het
Sry C A Y: 2,663,298 (GRCm39) A121S possibly damaging Het
Sspo C T 6: 48,462,386 (GRCm39) T3719I probably damaging Het
Tcap T C 11: 98,275,171 (GRCm39) S102P probably benign Het
Thap7 T C 16: 17,346,486 (GRCm39) R166G probably benign Het
Tmem229a T C 6: 24,955,580 (GRCm39) Y58C probably damaging Het
Trim8 A G 19: 46,504,059 (GRCm39) Y537C probably damaging Het
Ubr4 T A 4: 139,200,528 (GRCm39) M4692K unknown Het
Uvssa A G 5: 33,549,523 (GRCm39) S395G probably benign Het
Vgll4 G T 6: 114,867,695 (GRCm39) T52K probably damaging Het
Vmn2r7 A G 3: 64,600,527 (GRCm39) L548P probably benign Het
Vmn2r92 T A 17: 18,387,134 (GRCm39) S158T probably damaging Het
Wdr70 A T 15: 8,072,337 (GRCm39) probably benign Het
Zbtb48 A T 4: 152,105,344 (GRCm39) C463S probably 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
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
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'- TTCTCCTCAGCGTATGAAGCC -3'
(R):5'- ATGCACACTTCCTCTTGCAG -3'

Sequencing Primer
(F):5'- AGGTTGTGAAAATCTCCCCAGTG -3'
(R):5'- AGTTCGTGCATCACTCCTCAG -3'
Posted On 2020-07-28