Incidental Mutation 'R5931:Pcdha4'
ID 461882
Institutional Source Beutler Lab
Gene Symbol Pcdha4
Ensembl Gene ENSMUSG00000104252
Gene Name protocadherin alpha 4
Synonyms Crnr1, Cnr1
MMRRC Submission 044126-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.161) question?
Stock # R5931 (G1)
Quality Score 225
Status Not validated
Chromosome 18
Chromosomal Location 37085742-37320710 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 37087808 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Serine at position 664 (T664S)
Ref Sequence ENSEMBL: ENSMUSP00000141408 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000115661] [ENSMUST00000115662] [ENSMUST00000192295] [ENSMUST00000192503] [ENSMUST00000192512] [ENSMUST00000195590] [ENSMUST00000193839]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000070797
SMART Domains Protein: ENSMUSP00000068828
Gene: ENSMUSG00000103442

DomainStartEndE-ValueType
CA 22 132 3.09e-2 SMART
CA 156 241 6.14e-20 SMART
CA 265 349 3.92e-27 SMART
CA 373 454 4.94e-24 SMART
CA 478 564 1e-24 SMART
CA 592 672 4.55e-14 SMART
transmembrane domain 694 716 N/A INTRINSIC
Pfam:Cadherin_tail 797 931 5.3e-58 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000115661
AA Change: T664S

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458
AA Change: T664S

DomainStartEndE-ValueType
CA 20 131 5.3e-2 SMART
CA 155 240 1.51e-19 SMART
CA 264 348 7.6e-25 SMART
CA 372 453 1.42e-24 SMART
CA 477 563 1.42e-24 SMART
CA 594 674 4.12e-12 SMART
low complexity region 706 721 N/A INTRINSIC
Pfam:Cadherin_tail 796 930 3.9e-58 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000115662
SMART Domains Protein: ENSMUSP00000111326
Gene: ENSMUSG00000104148

DomainStartEndE-ValueType
CA 45 131 6.34e-2 SMART
CA 155 240 2.98e-18 SMART
CA 264 348 2.17e-29 SMART
CA 372 453 2.84e-24 SMART
CA 477 563 5.02e-25 SMART
CA 594 675 8.16e-16 SMART
transmembrane domain 695 717 N/A INTRINSIC
low complexity region 916 940 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000192295
SMART Domains Protein: ENSMUSP00000142103
Gene: ENSMUSG00000104252

DomainStartEndE-ValueType
CA 20 131 5.3e-2 SMART
CA 155 240 1.51e-19 SMART
CA 264 348 7.6e-25 SMART
CA 372 453 1.42e-24 SMART
CA 477 568 5.38e-1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000192503
SMART Domains Protein: ENSMUSP00000141989
Gene: ENSMUSG00000102312

DomainStartEndE-ValueType
low complexity region 11 17 N/A INTRINSIC
CA 42 128 3.78e-2 SMART
CA 152 237 8.94e-22 SMART
CA 261 345 3.74e-24 SMART
CA 369 450 1.09e-25 SMART
CA 474 560 1.42e-24 SMART
CA 588 670 2.96e-13 SMART
transmembrane domain 692 714 N/A INTRINSIC
low complexity region 910 934 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000192512
AA Change: T664S

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000141408
Gene: ENSMUSG00000104252
AA Change: T664S

DomainStartEndE-ValueType
CA 20 131 5.3e-2 SMART
CA 155 240 1.51e-19 SMART
CA 264 348 7.6e-25 SMART
CA 372 453 1.42e-24 SMART
CA 477 563 1.42e-24 SMART
CA 594 674 4.12e-12 SMART
low complexity region 706 721 N/A INTRINSIC
low complexity region 915 939 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000194235
Predicted Effect noncoding transcript
Transcript: ENSMUST00000194001
Predicted Effect probably benign
Transcript: ENSMUST00000195590
SMART Domains Protein: ENSMUSP00000141355
Gene: ENSMUSG00000104148

DomainStartEndE-ValueType
CA 45 131 6.34e-2 SMART
CA 155 240 2.98e-18 SMART
CA 264 348 2.17e-29 SMART
CA 372 453 2.84e-24 SMART
CA 477 563 5.02e-25 SMART
CA 594 675 8.16e-16 SMART
transmembrane domain 695 717 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000193839
SMART Domains Protein: ENSMUSP00000142308
Gene: ENSMUSG00000103442

DomainStartEndE-ValueType
CA 22 132 3.09e-2 SMART
CA 156 241 6.14e-20 SMART
CA 265 349 3.92e-27 SMART
CA 373 454 4.94e-24 SMART
CA 478 564 1e-24 SMART
CA 592 672 4.55e-14 SMART
transmembrane domain 694 716 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.1%
  • 20x: 94.4%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930590J08Rik A T 6: 91,896,096 (GRCm39) R315W probably damaging Het
Atrn A T 2: 130,775,356 (GRCm39) Y153F possibly damaging Het
C4b A G 17: 34,948,167 (GRCm39) V1644A probably damaging Het
Carmil3 A C 14: 55,736,397 (GRCm39) K654T probably damaging Het
Cdh1 T C 8: 107,392,964 (GRCm39) probably null Het
Chrna1 C T 2: 73,398,444 (GRCm39) V332M probably benign Het
Clca3a2 A C 3: 144,797,886 (GRCm39) V193G possibly damaging Het
Cyld A G 8: 89,456,470 (GRCm39) probably null Het
Dbt A T 3: 116,317,074 (GRCm39) E83D possibly damaging Het
Deup1 T C 9: 15,472,618 (GRCm39) R471G possibly damaging Het
Dgcr2 T A 16: 17,675,173 (GRCm39) I188F possibly damaging Het
Dgkg G A 16: 22,376,788 (GRCm39) R524* probably null Het
Dnaaf9 G A 2: 130,656,109 (GRCm39) T2M probably damaging Het
Dnah5 A T 15: 28,453,425 (GRCm39) R4399W probably damaging Het
Egflam G A 15: 7,273,338 (GRCm39) T579I possibly damaging Het
Eif2b2 C T 12: 85,269,561 (GRCm39) T211I probably damaging Het
Ep400 A G 5: 110,883,386 (GRCm39) probably benign Het
Ermp1 C G 19: 29,593,129 (GRCm39) A788P probably benign Het
Ern1 A G 11: 106,317,699 (GRCm39) S142P possibly damaging Het
Fbxo15 T A 18: 84,999,250 (GRCm39) C351S probably damaging Het
Fndc3a A T 14: 72,806,307 (GRCm39) S444T probably benign Het
Gabra6 G A 11: 42,198,268 (GRCm39) T384M probably benign Het
Gpbp1l1 T C 4: 116,447,457 (GRCm39) V379A probably benign Het
Hook2 G T 8: 85,722,375 (GRCm39) E305* probably null Het
Hoxa3 G A 6: 52,149,568 (GRCm39) A21V probably damaging Het
Hs1bp3 C A 12: 8,391,915 (GRCm39) P339Q probably benign Het
Igha T A 12: 113,223,710 (GRCm39) T49S probably benign Het
Klra4 C T 6: 130,030,016 (GRCm39) V190M possibly damaging Het
Lats2 A G 14: 57,933,588 (GRCm39) L843P probably damaging Het
Lcmt1 A G 7: 123,020,839 (GRCm39) T255A probably benign Het
Lpar6 A G 14: 73,476,368 (GRCm39) I110V probably damaging Het
Lrrtm4 A G 6: 79,998,722 (GRCm39) I44V probably damaging Het
Mcm3ap T C 10: 76,307,000 (GRCm39) V371A probably benign Het
Muc20 A T 16: 32,614,944 (GRCm39) D144E possibly damaging Het
Nphp3 T A 9: 103,897,945 (GRCm39) D417E probably damaging Het
Or7g33 A T 9: 19,448,629 (GRCm39) I199K probably benign Het
Or8b40 A G 9: 38,027,670 (GRCm39) I193V probably benign Het
Paqr7 A C 4: 134,235,031 (GRCm39) Y296S probably damaging Het
Pelo T A 13: 115,225,379 (GRCm39) Y282F probably benign Het
Plxna2 A T 1: 194,493,178 (GRCm39) I1818F probably damaging Het
Pnkd A G 1: 74,389,833 (GRCm39) D319G probably benign Het
Pnma8a C A 7: 16,694,809 (GRCm39) N221K probably benign Het
Ppp1cb T A 5: 32,640,810 (GRCm39) probably null Het
Prkca T G 11: 107,905,136 (GRCm39) I201L probably benign Het
Prp2rt A G 13: 97,235,705 (GRCm39) L14S probably benign Het
Rfx2 G A 17: 57,087,778 (GRCm39) R538C probably damaging Het
Rph3a T C 5: 121,101,936 (GRCm39) Q100R probably damaging Het
Rtel1 C T 2: 180,972,608 (GRCm39) R29* probably null Het
Scel T A 14: 103,843,060 (GRCm39) Y547* probably null Het
Sp100 C T 1: 85,606,804 (GRCm39) P303L probably damaging Het
Stk31 A G 6: 49,446,236 (GRCm39) S958G probably benign Het
Syne2 T A 12: 76,055,639 (GRCm39) V4168E probably benign Het
Tenm3 A T 8: 49,099,533 (GRCm39) S91T probably benign Het
Tmcc2 TTGCTGCTGCTGCTGCTGC TTGCTGCTGCTGCTGC 1: 132,285,493 (GRCm39) probably benign Het
Tmem248 T A 5: 130,258,349 (GRCm39) I14N probably damaging Het
Tor3a T C 1: 156,484,057 (GRCm39) I298V probably benign Het
Trim69 A T 2: 122,009,075 (GRCm39) K378N probably damaging Het
Ttc28 C T 5: 111,232,975 (GRCm39) P151S possibly damaging Het
Uaca T C 9: 60,779,294 (GRCm39) V1225A probably damaging Het
Vps4b T C 1: 106,705,065 (GRCm39) I343V probably benign Het
Wnk4 A G 11: 101,152,047 (GRCm39) T184A probably damaging Het
Ythdc2 T A 18: 45,006,023 (GRCm39) I1172K possibly damaging Het
Other mutations in Pcdha4
AlleleSourceChrCoordTypePredicted EffectPPH Score
R2570:Pcdha4 UTSW 18 37,086,665 (GRCm39) missense probably benign 0.00
R3114:Pcdha4 UTSW 18 37,086,603 (GRCm39) missense probably benign 0.02
R3115:Pcdha4 UTSW 18 37,086,603 (GRCm39) missense probably benign 0.02
R4154:Pcdha4 UTSW 18 37,086,639 (GRCm39) splice site probably null
R4381:Pcdha4 UTSW 18 37,085,928 (GRCm39) missense probably damaging 1.00
R4389:Pcdha4 UTSW 18 37,087,842 (GRCm39) missense probably benign
R4493:Pcdha4 UTSW 18 37,087,644 (GRCm39) missense possibly damaging 0.80
R4801:Pcdha4 UTSW 18 37,087,008 (GRCm39) nonsense probably null
R4802:Pcdha4 UTSW 18 37,087,008 (GRCm39) nonsense probably null
R4827:Pcdha4 UTSW 18 37,086,251 (GRCm39) missense probably damaging 1.00
R4928:Pcdha4 UTSW 18 37,087,869 (GRCm39) missense probably benign 0.01
R5001:Pcdha4 UTSW 18 37,088,001 (GRCm39) missense probably benign
R5330:Pcdha4 UTSW 18 37,087,755 (GRCm39) missense probably benign 0.01
R5331:Pcdha4 UTSW 18 37,087,755 (GRCm39) missense probably benign 0.01
R5540:Pcdha4 UTSW 18 37,087,890 (GRCm39) missense probably benign 0.01
R5587:Pcdha4 UTSW 18 37,087,875 (GRCm39) missense probably benign
R6249:Pcdha4 UTSW 18 37,086,729 (GRCm39) missense probably damaging 0.99
R6427:Pcdha4 UTSW 18 37,086,786 (GRCm39) missense probably benign 0.00
R6612:Pcdha4 UTSW 18 37,088,031 (GRCm39) missense probably benign 0.00
R6616:Pcdha4 UTSW 18 37,086,953 (GRCm39) missense probably benign
R7030:Pcdha4 UTSW 18 37,087,080 (GRCm39) missense probably damaging 1.00
R7198:Pcdha4 UTSW 18 37,086,613 (GRCm39) missense probably damaging 0.99
R7411:Pcdha4 UTSW 18 37,086,111 (GRCm39) missense probably benign 0.01
R7491:Pcdha4 UTSW 18 37,087,689 (GRCm39) missense probably damaging 1.00
R7513:Pcdha4 UTSW 18 37,086,392 (GRCm39) missense probably damaging 1.00
R7544:Pcdha4 UTSW 18 37,086,776 (GRCm39) missense probably benign 0.05
R7735:Pcdha4 UTSW 18 37,085,961 (GRCm39) missense probably damaging 1.00
R7753:Pcdha4 UTSW 18 37,086,354 (GRCm39) missense possibly damaging 0.49
R8104:Pcdha4 UTSW 18 37,087,106 (GRCm39) missense probably damaging 1.00
R8239:Pcdha4 UTSW 18 37,086,128 (GRCm39) missense probably damaging 1.00
R8767:Pcdha4 UTSW 18 37,086,905 (GRCm39) missense possibly damaging 0.73
R8802:Pcdha4 UTSW 18 37,087,211 (GRCm39) missense possibly damaging 0.91
R8869:Pcdha4 UTSW 18 37,086,011 (GRCm39) nonsense probably null
R9102:Pcdha4 UTSW 18 37,087,630 (GRCm39) missense probably damaging 1.00
R9365:Pcdha4 UTSW 18 37,087,112 (GRCm39) missense possibly damaging 0.92
R9593:Pcdha4 UTSW 18 37,086,740 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- CTTATGAGCTGCAATCGTCAG -3'
(R):5'- CACACCATTACCGGTTTTGGAG -3'

Sequencing Primer
(F):5'- TCGTCAGAAGGCAATTCCCGTAG -3'
(R):5'- TTTTGGAGGCCCGCACAC -3'
Posted On 2017-02-28