Incidental Mutation 'R7735:Pcdha4'
| ID |
596222 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha4
|
| Ensembl Gene |
ENSMUSG00000104252 |
| Gene Name |
protocadherin alpha 4 |
| Synonyms |
Crnr1, Cnr1 |
| MMRRC Submission |
045791-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.161)
|
| Stock # |
R7735 (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 G
at 37085961 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Serine
at position 48
(I48S)
|
| 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: I48S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458
AA Change: I48S
| 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 damaging
Transcript: ENSMUST00000192295
AA Change: I48S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000142103
Gene: ENSMUSG00000104252
AA Change: I48S
| 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: I48S
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000141408
Gene: ENSMUSG00000104252
AA Change: I48S
| 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: 99.9%
- 10x: 99.7%
- 20x: 99.1%
|
| Validation Efficiency |
100% (58/58) |
| 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: 58 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adcy8 |
T |
C |
15: 64,655,629 (GRCm39) |
T617A |
probably benign |
Het |
| Agl |
A |
T |
3: 116,578,795 (GRCm39) |
I446N |
probably benign |
Het |
| Aox1 |
C |
T |
1: 58,107,451 (GRCm39) |
P575L |
probably benign |
Het |
| Ap2m1 |
A |
T |
16: 20,358,269 (GRCm39) |
I96F |
probably benign |
Het |
| Arhgap15 |
A |
G |
2: 44,006,642 (GRCm39) |
D253G |
probably damaging |
Het |
| Arsa |
A |
T |
15: 89,359,152 (GRCm39) |
C171* |
probably null |
Het |
| Arsb |
G |
T |
13: 93,908,491 (GRCm39) |
R69L |
probably benign |
Het |
| Asb13 |
G |
A |
13: 3,684,180 (GRCm39) |
|
probably null |
Het |
| Canx |
G |
T |
11: 50,191,866 (GRCm39) |
D348E |
probably damaging |
Het |
| Cebpz |
C |
T |
17: 79,233,342 (GRCm39) |
|
probably null |
Het |
| Ces2h |
A |
T |
8: 105,741,127 (GRCm39) |
I40L |
probably benign |
Het |
| Cfhr4 |
A |
G |
1: 139,660,039 (GRCm39) |
|
probably null |
Het |
| Csmd2 |
T |
C |
4: 128,350,723 (GRCm39) |
|
probably null |
Het |
| Cxadr |
T |
A |
16: 78,125,949 (GRCm39) |
N106K |
possibly damaging |
Het |
| Ddo |
T |
C |
10: 40,507,770 (GRCm39) |
C56R |
probably benign |
Het |
| Dnah6 |
C |
T |
6: 73,046,412 (GRCm39) |
G3192D |
probably damaging |
Het |
| Efcab3 |
T |
A |
11: 104,962,465 (GRCm39) |
V49E |
probably benign |
Het |
| Epha10 |
T |
C |
4: 124,807,472 (GRCm39) |
Y578H |
|
Het |
| Fbxw16 |
T |
C |
9: 109,270,135 (GRCm39) |
D202G |
probably damaging |
Het |
| Gzf1 |
T |
C |
2: 148,530,083 (GRCm39) |
V538A |
possibly damaging |
Het |
| Igha |
T |
A |
12: 113,220,019 (GRCm39) |
|
probably benign |
Het |
| Iqce |
G |
T |
5: 140,663,839 (GRCm39) |
Q457K |
probably benign |
Het |
| Kbtbd3 |
A |
G |
9: 4,330,846 (GRCm39) |
K407E |
possibly damaging |
Het |
| Lipt1 |
A |
G |
1: 37,914,703 (GRCm39) |
E253G |
probably damaging |
Het |
| Mrnip |
G |
A |
11: 50,087,800 (GRCm39) |
W107* |
probably null |
Het |
| Mroh4 |
T |
C |
15: 74,497,357 (GRCm39) |
T224A |
probably damaging |
Het |
| Ncoa2 |
A |
T |
1: 13,218,661 (GRCm39) |
S1389R |
probably benign |
Het |
| Npffr2 |
A |
G |
5: 89,731,173 (GRCm39) |
I368V |
probably benign |
Het |
| Nrdc |
C |
T |
4: 108,895,182 (GRCm39) |
L469F |
probably damaging |
Het |
| Nup210l |
A |
T |
3: 90,092,883 (GRCm39) |
Q1279L |
probably damaging |
Het |
| Or4k47 |
T |
A |
2: 111,451,819 (GRCm39) |
N200I |
probably damaging |
Het |
| Or7e170 |
A |
G |
9: 19,795,410 (GRCm39) |
Y64H |
probably damaging |
Het |
| Pip5kl1 |
A |
G |
2: 32,469,101 (GRCm39) |
Y211C |
possibly damaging |
Het |
| Prrt4 |
A |
T |
6: 29,170,035 (GRCm39) |
S806T |
possibly damaging |
Het |
| Ptpn20 |
T |
A |
14: 33,352,902 (GRCm39) |
Y214N |
probably damaging |
Het |
| Ptprt |
A |
T |
2: 161,417,661 (GRCm39) |
N938K |
probably damaging |
Het |
| Scn2a |
G |
T |
2: 65,594,013 (GRCm39) |
V1621L |
probably benign |
Het |
| Senp3 |
A |
G |
11: 69,569,087 (GRCm39) |
I358T |
probably damaging |
Het |
| Sf3b1 |
A |
T |
1: 55,042,508 (GRCm39) |
S461T |
probably benign |
Het |
| Slc22a2 |
C |
T |
17: 12,828,917 (GRCm39) |
T341I |
probably damaging |
Het |
| Slc38a7 |
A |
T |
8: 96,568,295 (GRCm39) |
D363E |
probably benign |
Het |
| Slc6a5 |
T |
C |
7: 49,598,090 (GRCm39) |
|
probably null |
Het |
| Smo |
T |
A |
6: 29,759,851 (GRCm39) |
V650E |
probably damaging |
Het |
| Spata17 |
G |
A |
1: 186,872,577 (GRCm39) |
T31I |
unknown |
Het |
| Sstr2 |
T |
A |
11: 113,515,423 (GRCm39) |
I114N |
possibly damaging |
Het |
| Styxl1 |
T |
C |
5: 135,788,023 (GRCm39) |
Y146C |
probably damaging |
Het |
| Synpo2l |
T |
C |
14: 20,711,243 (GRCm39) |
Q688R |
possibly damaging |
Het |
| Tmem245 |
C |
T |
4: 56,925,155 (GRCm39) |
R322H |
probably benign |
Het |
| Tnxb |
A |
G |
17: 34,890,398 (GRCm39) |
E247G |
unknown |
Het |
| Ttc28 |
A |
T |
5: 111,414,544 (GRCm39) |
|
probably null |
Het |
| Ttn |
A |
T |
2: 76,718,416 (GRCm39) |
I7255N |
unknown |
Het |
| Ttn |
C |
A |
2: 76,652,768 (GRCm39) |
|
probably null |
Het |
| Unc13b |
C |
T |
4: 43,165,791 (GRCm39) |
R204C |
probably damaging |
Het |
| Utrn |
A |
G |
10: 12,619,787 (GRCm39) |
|
probably null |
Het |
| Vps53 |
A |
T |
11: 75,937,962 (GRCm39) |
F753I |
probably damaging |
Het |
| Ypel1 |
G |
T |
16: 16,918,124 (GRCm39) |
S97R |
probably benign |
Het |
| Zdbf2 |
A |
G |
1: 63,343,264 (GRCm39) |
T548A |
possibly damaging |
Het |
| Zfp747 |
G |
A |
7: 126,973,672 (GRCm39) |
T166M |
probably damaging |
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 |
|
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'- GCTCTGAGAGAATCCCTAATCAG -3'
(R):5'- CACGTGGAAAACCTGCAACG -3'
Sequencing Primer
(F):5'- TAATCAGAACAAAGCACTGTGC -3'
(R):5'- GGAAAACCTGCAACGGCCTG -3'
|
| Posted On |
2019-11-26 |
Incidental Mutation