Incidental Mutation 'R7411:Pcdha4'
| ID |
575114 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha4
|
| Ensembl Gene |
ENSMUSG00000104252 |
| Gene Name |
protocadherin alpha 4 |
| Synonyms |
Crnr1, Cnr1 |
| MMRRC Submission |
045492-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.161)
|
| Stock # |
R7411 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
18 |
| Chromosomal Location |
37085742-37320710 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to T
at 37086111 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Leucine
at position 98
(R98L)
|
| 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 benign
Transcript: ENSMUST00000115661
AA Change: R98L
PolyPhen 2
Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458
AA Change: R98L
| 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
AA Change: R98L
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000142103
Gene: ENSMUSG00000104252
AA Change: R98L
| 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 benign
Transcript: ENSMUST00000192512
AA Change: R98L
PolyPhen 2
Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)
|
| SMART Domains |
Protein: ENSMUSP00000141408
Gene: ENSMUSG00000104252
AA Change: R98L
| 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: 99.7%
- 20x: 99.1%
|
| 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: 70 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1810055G02Rik |
C |
T |
19: 3,767,241 (GRCm39) |
T276I |
possibly damaging |
Het |
| Abca17 |
A |
G |
17: 24,547,543 (GRCm39) |
I277T |
possibly damaging |
Het |
| Abcb11 |
C |
T |
2: 69,134,280 (GRCm39) |
|
probably null |
Het |
| Abcc12 |
C |
A |
8: 87,287,479 (GRCm39) |
R122L |
possibly damaging |
Het |
| Abcc8 |
A |
G |
7: 45,815,341 (GRCm39) |
|
probably null |
Het |
| Adam28 |
C |
T |
14: 68,864,396 (GRCm39) |
R469K |
probably damaging |
Het |
| Adamts18 |
T |
C |
8: 114,504,362 (GRCm39) |
Y243C |
probably damaging |
Het |
| Agbl3 |
T |
C |
6: 34,791,754 (GRCm39) |
S619P |
probably damaging |
Het |
| Alpk3 |
A |
T |
7: 80,742,600 (GRCm39) |
T806S |
probably benign |
Het |
| Armh3 |
A |
C |
19: 45,953,874 (GRCm39) |
V170G |
probably benign |
Het |
| Atoh1 |
T |
A |
6: 64,706,914 (GRCm39) |
I203N |
probably damaging |
Het |
| Cables1 |
A |
G |
18: 11,973,572 (GRCm39) |
E237G |
probably benign |
Het |
| Cacna1d |
A |
G |
14: 30,074,947 (GRCm39) |
M1T |
probably null |
Het |
| Ccdc91 |
C |
T |
6: 147,493,696 (GRCm39) |
Q363* |
probably null |
Het |
| Cdhr17 |
A |
T |
5: 17,029,763 (GRCm39) |
T500S |
possibly damaging |
Het |
| Ceacam5 |
T |
A |
7: 17,484,678 (GRCm39) |
D473E |
probably damaging |
Het |
| Cfap54 |
T |
A |
10: 92,704,617 (GRCm39) |
D2821V |
unknown |
Het |
| Clca3a2 |
A |
G |
3: 144,507,860 (GRCm39) |
S737P |
probably damaging |
Het |
| Clec4n |
T |
A |
6: 123,209,145 (GRCm39) |
M70K |
probably benign |
Het |
| Dnai3 |
A |
G |
3: 145,802,900 (GRCm39) |
V97A |
probably damaging |
Het |
| Dstyk |
G |
A |
1: 132,345,404 (GRCm39) |
G21S |
probably benign |
Het |
| Efcab3 |
T |
G |
11: 104,890,549 (GRCm39) |
N4210K |
probably benign |
Het |
| Enpp5 |
A |
G |
17: 44,392,366 (GRCm39) |
D265G |
probably damaging |
Het |
| Gabrb1 |
T |
C |
5: 72,279,538 (GRCm39) |
|
probably null |
Het |
| Gm40460 |
CACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAG |
CACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAG |
7: 141,794,554 (GRCm39) |
|
probably benign |
Het |
| Guk1 |
A |
G |
11: 59,076,811 (GRCm39) |
F91L |
|
Het |
| Ints1 |
C |
T |
5: 139,750,015 (GRCm39) |
E961K |
possibly damaging |
Het |
| Irx2 |
T |
A |
13: 72,777,182 (GRCm39) |
M1K |
probably null |
Het |
| Jrk |
C |
T |
15: 74,579,048 (GRCm39) |
R79H |
possibly damaging |
Het |
| Kcnu1 |
G |
T |
8: 26,382,116 (GRCm39) |
V489L |
probably damaging |
Het |
| Kctd7 |
C |
T |
5: 130,181,265 (GRCm39) |
T209M |
probably benign |
Het |
| Kdm5a |
T |
A |
6: 120,403,776 (GRCm39) |
V1127E |
probably damaging |
Het |
| Klk6 |
A |
G |
7: 43,476,367 (GRCm39) |
H69R |
probably damaging |
Het |
| Lck |
T |
C |
4: 129,445,763 (GRCm39) |
K340R |
probably benign |
Het |
| Lrrc75a |
A |
G |
11: 62,496,734 (GRCm39) |
L276P |
probably damaging |
Het |
| Med25 |
A |
G |
7: 44,527,667 (GRCm39) |
W730R |
probably damaging |
Het |
| Muc4 |
T |
C |
16: 32,570,140 (GRCm39) |
V400A |
probably benign |
Het |
| Myl10 |
G |
C |
5: 136,726,825 (GRCm39) |
V70L |
probably benign |
Het |
| Myt1 |
C |
A |
2: 181,456,899 (GRCm39) |
H906Q |
probably damaging |
Het |
| Ncl |
A |
T |
1: 86,278,564 (GRCm39) |
F673I |
probably damaging |
Het |
| Nfe2l1 |
G |
T |
11: 96,713,009 (GRCm39) |
T216N |
probably benign |
Het |
| Nos2 |
G |
A |
11: 78,835,681 (GRCm39) |
|
probably null |
Het |
| Nphp4 |
T |
A |
4: 152,639,174 (GRCm39) |
I935N |
probably benign |
Het |
| Ntn1 |
G |
A |
11: 68,276,915 (GRCm39) |
A11V |
probably benign |
Het |
| Or2t26 |
A |
T |
11: 49,039,821 (GRCm39) |
M246L |
probably benign |
Het |
| Or4c10b |
T |
C |
2: 89,711,605 (GRCm39) |
V145A |
probably damaging |
Het |
| Pate11 |
T |
C |
9: 36,386,980 (GRCm39) |
V16A |
possibly damaging |
Het |
| Pcdha12 |
A |
G |
18: 37,154,661 (GRCm39) |
Y460C |
probably damaging |
Het |
| Pitpnc1 |
A |
G |
11: 107,103,398 (GRCm39) |
S234P |
probably damaging |
Het |
| Pmfbp1 |
A |
T |
8: 110,240,503 (GRCm39) |
Y195F |
probably damaging |
Het |
| Prl6a1 |
T |
C |
13: 27,502,125 (GRCm39) |
I164T |
probably damaging |
Het |
| Ptpn18 |
G |
A |
1: 34,511,273 (GRCm39) |
|
probably null |
Het |
| Rhbdl2 |
G |
A |
4: 123,723,435 (GRCm39) |
A280T |
possibly damaging |
Het |
| Rsf1 |
CGGC |
CGGCGGCGGGGGC |
7: 97,229,139 (GRCm39) |
|
probably benign |
Het |
| Sema3a |
T |
G |
5: 13,566,230 (GRCm39) |
Y171* |
probably null |
Het |
| Set |
A |
G |
2: 29,956,897 (GRCm39) |
E22G |
probably benign |
Het |
| Sirpb1b |
A |
T |
3: 15,608,057 (GRCm39) |
D229E |
probably benign |
Het |
| Slc12a2 |
A |
T |
18: 58,074,085 (GRCm39) |
I1096F |
probably benign |
Het |
| Slc30a5 |
T |
C |
13: 100,954,688 (GRCm39) |
I159V |
probably benign |
Het |
| Slc35f3 |
CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC |
CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC |
8: 127,115,777 (GRCm39) |
|
probably benign |
Het |
| Slc6a20b |
A |
G |
9: 123,434,013 (GRCm39) |
I275T |
probably benign |
Het |
| Speer1e |
T |
A |
5: 11,233,116 (GRCm39) |
|
probably null |
Het |
| Stradb |
A |
C |
1: 59,027,677 (GRCm39) |
D69A |
possibly damaging |
Het |
| Supt16 |
A |
T |
14: 52,415,508 (GRCm39) |
V409E |
probably damaging |
Het |
| Tcea2 |
A |
G |
2: 181,328,457 (GRCm39) |
N195S |
probably damaging |
Het |
| Thumpd3 |
T |
C |
6: 113,033,072 (GRCm39) |
V270A |
possibly damaging |
Het |
| Urgcp |
T |
A |
11: 5,668,116 (GRCm39) |
H117L |
probably benign |
Het |
| Vps13c |
T |
A |
9: 67,879,283 (GRCm39) |
M3408K |
probably damaging |
Het |
| Wdfy4 |
A |
C |
14: 32,828,088 (GRCm39) |
M1078R |
|
Het |
| Ypel5 |
G |
A |
17: 73,153,439 (GRCm39) |
|
probably null |
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 |
|
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'- ATCCACTACTCCATCCCTGAGG -3'
(R):5'- ATTCCGATATCTGCGTCTGAAGC -3'
Sequencing Primer
(F):5'- TCCCTGAGGAGGCCAAAC -3'
(R):5'- TGAAGCGCCCTCTAGTGGAAAC -3'
|
| Posted On |
2019-10-07 |
Incidental Mutation