Incidental Mutation 'R3926:Pcdh9'
ID 308300
Institutional Source Beutler Lab
Gene Symbol Pcdh9
Ensembl Gene ENSMUSG00000055421
Gene Name protocadherin 9
Synonyms C630029H24Rik, LOC382930, A730003J17Rik, 1500001L12Rik, C530050I23Rik
MMRRC Submission 040821-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.166) question?
Stock # R3926 (G1)
Quality Score 225
Status Validated
Chromosome 14
Chromosomal Location 93250846-94128115 bp(-) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) G to T at 94124246 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Stop codon at position 641 (Y641*)
Ref Sequence ENSEMBL: ENSMUSP00000141396 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000068992] [ENSMUST00000192221] [ENSMUST00000193901] [ENSMUST00000194056] [ENSMUST00000195376] [ENSMUST00000195826]
AlphaFold F8VPK8
Predicted Effect probably null
Transcript: ENSMUST00000068992
AA Change: Y641*
SMART Domains Protein: ENSMUSP00000070935
Gene: ENSMUSG00000055421
AA Change: Y641*

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 null
Transcript: ENSMUST00000192221
AA Change: Y518*
SMART Domains Protein: ENSMUSP00000142260
Gene: ENSMUSG00000055421
AA Change: Y518*

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 null
Transcript: ENSMUST00000193901
AA Change: Y641*
SMART Domains Protein: ENSMUSP00000141759
Gene: ENSMUSG00000055421
AA Change: Y641*

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 null
Transcript: ENSMUST00000194056
AA Change: Y641*
SMART Domains Protein: ENSMUSP00000141602
Gene: ENSMUSG00000055421
AA Change: Y641*

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 null
Transcript: ENSMUST00000195376
AA Change: Y641*
SMART Domains Protein: ENSMUSP00000142224
Gene: ENSMUSG00000055421
AA Change: Y641*

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 null
Transcript: ENSMUST00000195826
AA Change: Y641*
SMART Domains Protein: ENSMUSP00000141396
Gene: ENSMUSG00000055421
AA Change: Y641*

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 0.9753 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 93.6%
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
1700012B07Rik G T 11: 109,684,980 (GRCm39) C172* probably null Het
Ahnak G A 19: 8,983,692 (GRCm39) D1659N probably benign Het
Arfgap2 C T 2: 91,105,150 (GRCm39) R405W probably damaging Het
Asb14 T C 14: 26,619,695 (GRCm39) I48T possibly damaging Het
Astn1 A T 1: 158,407,227 (GRCm39) I559F possibly damaging Het
Atg7 C T 6: 114,650,639 (GRCm39) T83M possibly damaging Het
Bco1 T C 8: 117,854,211 (GRCm39) S379P probably benign Het
Becn2 T C 1: 175,748,852 (GRCm39) V306A probably benign Het
Bst1 T C 5: 43,997,796 (GRCm39) V265A possibly damaging Het
Car11 T C 7: 45,349,915 (GRCm39) F45L probably benign Het
Cdkl2 T C 5: 92,180,998 (GRCm39) I214V possibly damaging Het
Cluap1 T A 16: 3,729,398 (GRCm39) S141T probably damaging Het
Col11a1 C T 3: 113,883,773 (GRCm39) probably benign Het
Col1a2 G A 6: 4,518,822 (GRCm39) probably benign Het
Corin T G 5: 72,529,473 (GRCm39) D294A probably damaging Het
Crct1 C A 3: 92,922,014 (GRCm39) probably benign Het
Ddx41 A G 13: 55,679,083 (GRCm39) L559P probably damaging Het
Ddx59 T A 1: 136,344,482 (GRCm39) V51D probably benign Het
Dennd1b A G 1: 139,071,697 (GRCm39) N397D probably benign Het
Evc2 T A 5: 37,540,574 (GRCm39) L590Q probably damaging Het
Fhl5 A T 4: 25,214,790 (GRCm39) probably benign Het
Flg2 A G 3: 93,110,522 (GRCm39) Y850C unknown Het
Gal3st2b G T 1: 93,868,512 (GRCm39) V246L probably benign Het
Jam3 A T 9: 27,017,701 (GRCm39) I29K possibly damaging Het
Klhl1 A T 14: 96,584,316 (GRCm39) C305S possibly damaging Het
Lims2 A G 18: 32,090,996 (GRCm39) S327G probably benign Het
Lynx1 A G 15: 74,623,205 (GRCm39) Y76H probably damaging Het
Mycbp2 G A 14: 103,441,936 (GRCm39) P1943L probably damaging Het
Myo3a A G 2: 22,455,053 (GRCm39) D86G probably damaging Het
Nkx3-2 T A 5: 41,919,223 (GRCm39) Q255L probably damaging Het
Notch3 C T 17: 32,372,531 (GRCm39) R641H possibly damaging Het
Nr2c2 T A 6: 92,137,382 (GRCm39) M431K probably damaging Het
Ogfod3 T C 11: 121,074,255 (GRCm39) T265A probably damaging Het
Pcdha9 T A 18: 37,132,465 (GRCm39) D511E probably damaging Het
Pcdhgb8 A G 18: 37,895,443 (GRCm39) Y171C probably damaging Het
Pcnx1 T C 12: 82,005,505 (GRCm39) C1075R probably damaging Het
Pik3c3 C A 18: 30,444,382 (GRCm39) probably benign Het
Pkhd1 T C 1: 20,621,097 (GRCm39) T854A probably benign Het
Pycr1 T C 11: 120,532,961 (GRCm39) T100A probably benign Het
Rhof T C 5: 123,242,593 (GRCm39) probably null Het
Scn9a T A 2: 66,357,217 (GRCm39) D1028V possibly damaging Het
Serpina3f T C 12: 104,185,740 (GRCm39) I315T possibly damaging Het
Slc1a6 T A 10: 78,648,715 (GRCm39) S479T possibly damaging Het
Tmcc1 T C 6: 116,019,874 (GRCm39) D166G probably damaging Het
Trav3-3 A G 14: 53,903,828 (GRCm39) K49E probably benign Het
Usp28 T C 9: 48,942,223 (GRCm39) probably null Het
Utrn C T 10: 12,573,786 (GRCm39) V1095I probably benign Het
Zfp217 T C 2: 169,954,438 (GRCm39) D1038G probably damaging Het
Zfp709 A G 8: 72,644,397 (GRCm39) R609G probably damaging Het
Zfp729a T A 13: 67,768,310 (GRCm39) K640* probably null Het
Zfp986 A T 4: 145,619,090 (GRCm39) probably benign Het
Zkscan6 A T 11: 65,719,051 (GRCm39) H357L 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
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'- GTTCTGCATTCATTCCGGTG -3'
(R):5'- TTTGTGTCTGAGAATCTGCCAAAG -3'

Sequencing Primer
(F):5'- GCATTCATTCCGGTGTCAATATC -3'
(R):5'- GTGTCTGAGAATCTGCCAAAGTATAG -3'
Posted On 2015-04-17