Incidental Mutation 'R9102:Pcdha4'
| ID |
691786 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha4
|
| Ensembl Gene |
ENSMUSG00000104252 |
| Gene Name |
protocadherin alpha 4 |
| Synonyms |
Crnr1, Cnr1 |
| MMRRC Submission |
068916-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.161)
|
| Stock # |
R9102 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
37085742-37320710 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 37087630 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Lysine
at position 604
(N604K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000141408
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000070797]
[ENSMUST00000115661]
[ENSMUST00000115662]
[ENSMUST00000192295]
[ENSMUST00000192503]
[ENSMUST00000192512]
[ENSMUST00000193839]
[ENSMUST00000195590]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000070797
|
| SMART Domains |
Protein: ENSMUSP00000068828
Gene: ENSMUSG00000103442
| Domain | Start | End | E-Value | Type |
|---|
|
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: N604K
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458
AA Change: N604K
| Domain | Start | End | E-Value | Type |
|---|
|
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
| Domain | Start | End | E-Value | Type |
|---|
|
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
| Domain | Start | End | E-Value | Type |
|---|
|
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
| Domain | Start | End | E-Value | Type |
|---|
|
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: N604K
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000141408
Gene: ENSMUSG00000104252
AA Change: N604K
| Domain | Start | End | E-Value | Type |
|---|
|
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 |
probably benign
Transcript: ENSMUST00000193839
|
| SMART Domains |
Protein: ENSMUSP00000142308
Gene: ENSMUSG00000103442
| Domain | Start | End | E-Value | Type |
|---|
|
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 |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000195590
|
| SMART Domains |
Protein: ENSMUSP00000141355
Gene: ENSMUSG00000104148
| Domain | Start | End | E-Value | Type |
|---|
|
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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.3%
|
| Validation Efficiency |
97% (62/64) |
| 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: 63 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb9 |
T |
C |
5: 124,228,176 (GRCm39) |
T22A |
possibly damaging |
Het |
| Adam33 |
T |
C |
2: 130,897,737 (GRCm39) |
Q227R |
probably benign |
Het |
| Adgrb2 |
G |
A |
4: 129,912,802 (GRCm39) |
G1276D |
probably benign |
Het |
| Adra1b |
A |
G |
11: 43,667,056 (GRCm39) |
S394P |
possibly damaging |
Het |
| Arap2 |
T |
A |
5: 62,906,341 (GRCm39) |
H226L |
probably benign |
Het |
| Bckdk |
A |
G |
7: 127,506,658 (GRCm39) |
D297G |
probably null |
Het |
| Brwd1 |
T |
C |
16: 95,869,725 (GRCm39) |
T101A |
probably benign |
Het |
| Ciita |
A |
G |
16: 10,324,565 (GRCm39) |
R166G |
probably benign |
Het |
| Cnksr1 |
A |
G |
4: 133,956,323 (GRCm39) |
F587S |
probably damaging |
Het |
| Col4a1 |
A |
T |
8: 11,253,007 (GRCm39) |
C1548S |
possibly damaging |
Het |
| Cxcl15 |
G |
T |
5: 90,949,154 (GRCm39) |
M106I |
|
Het |
| Dennd6a |
T |
C |
14: 26,350,689 (GRCm39) |
I598T |
probably damaging |
Het |
| Dlg5 |
G |
A |
14: 24,199,567 (GRCm39) |
P1446S |
probably damaging |
Het |
| Dnah6 |
A |
T |
6: 73,044,469 (GRCm39) |
I3214N |
probably benign |
Het |
| Dnmt3b |
T |
C |
2: 153,518,703 (GRCm39) |
V622A |
probably damaging |
Het |
| Fam170b |
T |
A |
14: 32,557,404 (GRCm39) |
S80T |
probably damaging |
Het |
| Fbxl13 |
G |
T |
5: 21,837,801 (GRCm39) |
H45Q |
probably benign |
Het |
| Fbxo39 |
T |
C |
11: 72,208,316 (GRCm39) |
F223L |
possibly damaging |
Het |
| Fndc3b |
C |
A |
3: 27,523,014 (GRCm39) |
|
probably null |
Het |
| Gbp3 |
G |
C |
3: 142,273,586 (GRCm39) |
V378L |
probably benign |
Het |
| Gc |
C |
T |
5: 89,591,444 (GRCm39) |
S98N |
probably benign |
Het |
| Gck |
A |
G |
11: 5,856,516 (GRCm39) |
Y214H |
probably damaging |
Het |
| Gpr158 |
A |
T |
2: 21,830,078 (GRCm39) |
S708C |
probably damaging |
Het |
| Hmcn1 |
A |
T |
1: 150,573,331 (GRCm39) |
M2106K |
probably benign |
Het |
| Hoxd11 |
T |
A |
2: 74,513,274 (GRCm39) |
Y180N |
possibly damaging |
Het |
| Hydin |
A |
G |
8: 111,235,546 (GRCm39) |
I1844V |
probably benign |
Het |
| Knl1 |
T |
C |
2: 118,917,973 (GRCm39) |
I1777T |
probably benign |
Het |
| Krt33b |
A |
C |
11: 99,915,846 (GRCm39) |
L300R |
probably damaging |
Het |
| Madd |
C |
T |
2: 90,988,404 (GRCm39) |
A1208T |
probably benign |
Het |
| Meis2 |
T |
A |
2: 115,694,760 (GRCm39) |
N461I |
probably benign |
Het |
| Mgat1 |
T |
A |
11: 49,152,165 (GRCm39) |
V216E |
probably damaging |
Het |
| Nox4 |
G |
A |
7: 87,025,448 (GRCm39) |
R525Q |
probably benign |
Het |
| Npc1l1 |
C |
T |
11: 6,164,684 (GRCm39) |
V1122M |
possibly damaging |
Het |
| Nrsn1 |
A |
G |
13: 25,437,517 (GRCm39) |
M137T |
probably benign |
Het |
| Nrxn3 |
T |
C |
12: 90,298,924 (GRCm39) |
S1015P |
probably benign |
Het |
| Nudt22 |
T |
A |
19: 6,972,119 (GRCm39) |
I166F |
probably benign |
Het |
| Or10d1b |
A |
C |
9: 39,613,984 (GRCm39) |
V27G |
probably benign |
Het |
| Or5j1 |
C |
T |
2: 86,879,171 (GRCm39) |
M136I |
possibly damaging |
Het |
| Or6k4 |
A |
T |
1: 173,964,322 (GRCm39) |
N4I |
|
Het |
| Or6n2 |
T |
A |
1: 173,897,176 (GRCm39) |
F104Y |
probably damaging |
Het |
| Or8b4 |
T |
A |
9: 37,829,992 (GRCm39) |
I13N |
probably damaging |
Het |
| Or8g31-ps1 |
C |
T |
9: 39,276,388 (GRCm39) |
P178S |
unknown |
Het |
| Plxnc1 |
C |
T |
10: 94,663,107 (GRCm39) |
V1181M |
probably damaging |
Het |
| Pms1 |
G |
C |
1: 53,307,021 (GRCm39) |
H128Q |
probably benign |
Het |
| Prkar2b |
G |
A |
12: 32,013,025 (GRCm39) |
H364Y |
probably benign |
Het |
| Pus7 |
A |
T |
5: 23,957,380 (GRCm39) |
I357K |
possibly damaging |
Het |
| Rsf1 |
GCGGC |
GCGGCGGCGCCGGC |
7: 97,229,138 (GRCm39) |
|
probably benign |
Het |
| Ryr3 |
T |
C |
2: 112,508,906 (GRCm39) |
|
probably benign |
Het |
| Siglec1 |
T |
C |
2: 130,915,389 (GRCm39) |
I1401V |
probably benign |
Het |
| Slc6a6 |
G |
T |
6: 91,731,940 (GRCm39) |
V590L |
probably benign |
Het |
| Slc9b1 |
C |
T |
3: 135,100,725 (GRCm39) |
P490L |
probably damaging |
Het |
| Sprn |
T |
C |
7: 139,733,278 (GRCm39) |
D98G |
possibly damaging |
Het |
| Srrm4 |
T |
C |
5: 116,620,563 (GRCm39) |
D55G |
unknown |
Het |
| Sugct |
A |
G |
13: 17,497,833 (GRCm39) |
V280A |
probably benign |
Het |
| Tbx6 |
A |
G |
7: 126,381,014 (GRCm39) |
E83G |
possibly damaging |
Het |
| Tmem120a |
T |
C |
5: 135,765,455 (GRCm39) |
T209A |
probably benign |
Het |
| Top3a |
T |
C |
11: 60,647,155 (GRCm39) |
R255G |
probably damaging |
Het |
| Trav6-1 |
T |
A |
14: 52,876,008 (GRCm39) |
F13I |
probably benign |
Het |
| Tsnaxip1 |
A |
G |
8: 106,568,622 (GRCm39) |
E410G |
probably benign |
Het |
| Ubr5 |
A |
G |
15: 38,018,596 (GRCm39) |
V842A |
|
Het |
| Ubtf |
A |
G |
11: 102,201,015 (GRCm39) |
|
probably null |
Het |
| Vwa3b |
G |
A |
1: 37,174,593 (GRCm39) |
M1I |
probably null |
Het |
| Zfp518b |
T |
C |
5: 38,831,181 (GRCm39) |
T275A |
probably benign |
Het |
|
| Other mutations in Pcdha4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
|
|
R5931:Pcdha4
|
UTSW |
18 |
37,087,808 (GRCm39) |
missense |
probably damaging |
1.00 |
|
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 |
|
|
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'- AGCAATGTGACTCTGCAGG -3'
(R):5'- GATACTCGCGATGGAGCCTTTG -3'
Sequencing Primer
(F):5'- CAATGTGACTCTGCAGGTGTTTG -3'
(R):5'- CACTGTGGCGGTAACAATCATTG -3'
|
| Posted On |
2021-12-30 |
Incidental Mutation