Incidental Mutation 'R1622:Pcdh9'
ID 174732
Institutional Source Beutler Lab
Gene Symbol Pcdh9
Ensembl Gene ENSMUSG00000055421
Gene Name protocadherin 9
Synonyms C630029H24Rik, LOC382930, A730003J17Rik, 1500001L12Rik, C530050I23Rik
MMRRC Submission 039659-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.166) question?
Stock # R1622 (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 94123311 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 953 (D953G)
Ref Sequence ENSEMBL: ENSMUSP00000142224 (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: D953G

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000070935
Gene: ENSMUSG00000055421
AA Change: D953G

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: D830G

PolyPhen 2 Score 0.031 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000142260
Gene: ENSMUSG00000055421
AA Change: D830G

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: D953G

PolyPhen 2 Score 0.031 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000141759
Gene: ENSMUSG00000055421
AA Change: D953G

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
SMART Domains Protein: ENSMUSP00000141602
Gene: ENSMUSG00000055421

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: D953G

PolyPhen 2 Score 0.031 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000142224
Gene: ENSMUSG00000055421
AA Change: D953G

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: D953G

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000141396
Gene: ENSMUSG00000055421
AA Change: D953G

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 0.1565 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.6%
  • 20x: 93.3%
Validation Efficiency 98% (55/56)
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
Aldoart2 A G 12: 55,612,696 (GRCm39) E207G probably benign Het
Arhgap19 T A 19: 41,790,412 (GRCm39) S19C probably benign Het
Arhgef18 T A 8: 3,491,272 (GRCm39) D374E possibly damaging Het
Atf2 A G 2: 73,684,133 (GRCm39) probably null Het
Cadm1 A G 9: 47,725,139 (GRCm39) N300S probably benign Het
Ccdc159 A T 9: 21,840,666 (GRCm39) I78F possibly damaging Het
Cdh4 T C 2: 179,530,885 (GRCm39) I589T possibly damaging Het
Clstn1 T C 4: 149,713,864 (GRCm39) I182T probably damaging Het
Cnga3 T A 1: 37,283,909 (GRCm39) probably benign Het
Cntln T A 4: 84,981,418 (GRCm39) S865R probably damaging Het
Col5a3 C T 9: 20,683,516 (GRCm39) G1552E unknown Het
Col6a4 A C 9: 105,874,334 (GRCm39) S2218A probably benign Het
Ephb1 T C 9: 101,878,910 (GRCm39) T527A probably benign Het
Fkbp15 T A 4: 62,241,439 (GRCm39) I569F possibly damaging Het
Gabra4 A G 5: 71,729,329 (GRCm39) S484P possibly damaging Het
Glce T C 9: 61,977,843 (GRCm39) I14V possibly damaging Het
Gm4884 A T 7: 40,692,265 (GRCm39) Q78L probably damaging Het
Gpn1 A G 5: 31,660,748 (GRCm39) T180A possibly damaging Het
Gpr6 A T 10: 40,947,288 (GRCm39) I98N probably damaging Het
Hcrtr2 T C 9: 76,230,722 (GRCm39) N22S probably benign Het
Hfm1 C T 5: 107,041,389 (GRCm39) V665I possibly damaging Het
Il4ra T A 7: 125,169,225 (GRCm39) I159N possibly damaging Het
Irf8 G C 8: 121,466,561 (GRCm39) C2S possibly damaging Het
Itih2 A T 2: 10,106,890 (GRCm39) N701K probably benign Het
Lrrc4b GAGAAG GAG 7: 44,111,654 (GRCm39) probably benign Het
Mmp10 T A 9: 7,504,996 (GRCm39) Y263* probably null Het
Morc3 T A 16: 93,671,694 (GRCm39) M835K probably benign Het
Msh3 A G 13: 92,481,462 (GRCm39) probably null Het
Ncbp1 A G 4: 46,171,963 (GRCm39) H777R possibly damaging Het
Nfatc1 A G 18: 80,710,182 (GRCm39) M514T probably damaging Het
Nlrp3 T A 11: 59,439,302 (GRCm39) I293N probably damaging Het
Pank2 A T 2: 131,115,889 (GRCm39) E102D probably damaging Het
Pbrm1 A G 14: 30,754,505 (GRCm39) D175G probably benign Het
Pibf1 G A 14: 99,423,917 (GRCm39) V497I probably benign Het
Pkd1 G A 17: 24,800,614 (GRCm39) M3085I probably benign Het
Prss58 A T 6: 40,874,248 (GRCm39) C143S possibly damaging Het
Rassf8 A G 6: 145,765,829 (GRCm39) probably benign Het
Sp140l2 A G 1: 85,231,907 (GRCm39) probably benign Het
Spag7 T A 11: 70,555,688 (GRCm39) D73V probably damaging Het
Sult3a1 A T 10: 33,746,246 (GRCm39) M189L probably benign Het
Syt4 T C 18: 31,577,069 (GRCm39) D95G probably damaging Het
Tbc1d8 A C 1: 39,419,317 (GRCm39) S766A probably benign Het
Tmco5 A T 2: 116,710,796 (GRCm39) M39L probably benign Het
Trcg1 A G 9: 57,155,955 (GRCm39) N797S possibly damaging Het
Trim34a A T 7: 103,910,545 (GRCm39) probably null Het
Ubr5 T C 15: 38,009,357 (GRCm39) probably benign Het
Urb2 A G 8: 124,756,363 (GRCm39) N690S probably benign Het
Zfp445 A G 9: 122,681,614 (GRCm39) Y776H possibly damaging Het
Zfp52 G A 17: 21,781,833 (GRCm39) M560I probably benign Het
Zfp608 A G 18: 55,121,366 (GRCm39) S74P probably benign Het
Zfp629 A G 7: 127,211,012 (GRCm39) C266R probably damaging Het
Zscan2 A G 7: 80,525,134 (GRCm39) K285R 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
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
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'- TTGCCACTTGAAGGAAACTGGGAG -3'
(R):5'- TGAAGAGTCCAAACCCGATGATGC -3'

Sequencing Primer
(F):5'- ATTCTTGACTGAGCCCCAGAG -3'
(R):5'- AACCCGATGATGCCGTTC -3'
Posted On 2014-04-24