Incidental Mutation 'R4381:Pcdha4'
| ID |
325351 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha4
|
| Ensembl Gene |
ENSMUSG00000104252 |
| Gene Name |
protocadherin alpha 4 |
| Synonyms |
Crnr1, Cnr1 |
| MMRRC Submission |
041122-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.161)
|
| Stock # |
R4381 (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 G
at 37085928 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamic Acid to Glycine
at position 37
(E37G)
|
| 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: E37G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458
AA Change: E37G
| 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: E37G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000142103
Gene: ENSMUSG00000104252
AA Change: E37G
| 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: E37G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000141408
Gene: ENSMUSG00000104252
AA Change: E37G
| 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 |
noncoding transcript
Transcript: ENSMUST00000194001
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000194235
|
| 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: 99.2%
- 3x: 98.5%
- 10x: 96.9%
- 20x: 94.1%
|
| Validation Efficiency |
95% (41/43) |
| 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: 33 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Alpk1 |
C |
T |
3: 127,523,022 (GRCm39) |
V7M |
probably damaging |
Het |
| Dlgap2 |
A |
G |
8: 14,896,502 (GRCm39) |
I993V |
probably benign |
Het |
| Dst |
T |
C |
1: 34,202,316 (GRCm39) |
S215P |
probably damaging |
Het |
| Eml5 |
A |
G |
12: 98,782,214 (GRCm39) |
I1359T |
possibly damaging |
Het |
| Eps15 |
G |
A |
4: 109,223,727 (GRCm39) |
|
probably benign |
Het |
| Gpr158 |
T |
A |
2: 21,832,403 (GRCm39) |
W1168R |
probably damaging |
Het |
| Ighv1-62-1 |
T |
A |
12: 115,350,613 (GRCm39) |
H18L |
probably benign |
Het |
| Il18r1 |
A |
G |
1: 40,510,950 (GRCm39) |
I12V |
probably benign |
Het |
| Klk14 |
G |
A |
7: 43,341,501 (GRCm39) |
C51Y |
probably damaging |
Het |
| Mib2 |
G |
C |
4: 155,742,069 (GRCm39) |
A234G |
possibly damaging |
Het |
| Mtpap |
T |
C |
18: 4,383,223 (GRCm39) |
F200S |
probably benign |
Het |
| Nacad |
T |
A |
11: 6,550,204 (GRCm39) |
T996S |
probably benign |
Het |
| Nek9 |
T |
A |
12: 85,376,632 (GRCm39) |
T250S |
probably damaging |
Het |
| Nif3l1 |
A |
C |
1: 58,494,738 (GRCm39) |
|
probably benign |
Het |
| Nipbl |
A |
G |
15: 8,388,690 (GRCm39) |
V310A |
probably benign |
Het |
| Or10al3 |
G |
T |
17: 38,011,790 (GRCm39) |
E76D |
probably damaging |
Het |
| Or7g34 |
A |
G |
9: 19,478,038 (GRCm39) |
L211P |
probably benign |
Het |
| Pbrm1 |
T |
C |
14: 30,747,513 (GRCm39) |
V33A |
probably benign |
Het |
| Pdgfc |
A |
G |
3: 81,116,558 (GRCm39) |
K304R |
probably damaging |
Het |
| Peak1 |
G |
T |
9: 56,165,711 (GRCm39) |
A739E |
probably benign |
Het |
| Pla2g4c |
A |
T |
7: 13,079,990 (GRCm39) |
N433Y |
probably damaging |
Het |
| Polrmt |
A |
C |
10: 79,577,642 (GRCm39) |
L319R |
possibly damaging |
Het |
| Prkaa1 |
A |
T |
15: 5,206,289 (GRCm39) |
T373S |
probably benign |
Het |
| Qars1 |
G |
A |
9: 108,387,382 (GRCm39) |
|
probably benign |
Het |
| Ranbp1 |
G |
A |
16: 18,065,208 (GRCm39) |
L33F |
probably damaging |
Het |
| Rpgrip1 |
C |
T |
14: 52,387,906 (GRCm39) |
P1094L |
possibly damaging |
Het |
| Taf1d |
T |
A |
9: 15,223,277 (GRCm39) |
|
probably benign |
Het |
| Tstd2 |
T |
C |
4: 46,119,933 (GRCm39) |
K340E |
probably benign |
Het |
| Vmn2r45 |
A |
T |
7: 8,474,912 (GRCm39) |
C705* |
probably null |
Het |
| Vrk3 |
C |
T |
7: 44,424,866 (GRCm39) |
T427M |
probably benign |
Het |
| Zdhhc16 |
A |
G |
19: 41,929,093 (GRCm39) |
Y232C |
possibly damaging |
Het |
| Zfp1 |
T |
A |
8: 112,397,083 (GRCm39) |
L354Q |
probably damaging |
Het |
| Zyg11a |
G |
A |
4: 108,058,517 (GRCm39) |
A341V |
possibly 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 |
|
|
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 |
|
|
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'- ACGGATTAGAAGAATTCTCCTAGCTC -3'
(R):5'- ACGTGGAAAACCTGCAACG -3'
Sequencing Primer
(F):5'- GAATTCTCCTAGCTCTGAGAGAATCC -3'
(R):5'- TCCAGGTGGATGCTGCACTC -3'
|
| Posted On |
2015-07-06 |
Incidental Mutation