Incidental Mutation 'R8869:Pcdha4'
ID |
676164 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Pcdha4
|
Ensembl Gene |
ENSMUSG00000104252 |
Gene Name |
protocadherin alpha 4 |
Synonyms |
Crnr1, Cnr1 |
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.172)
|
Stock # |
R8869 (G1)
|
Quality Score |
225.009 |
Status
|
Not validated
|
Chromosome |
18 |
Chromosomal Location |
37085742-37320710 bp(+) (GRCm39) |
Type of Mutation |
nonsense |
DNA Base Change (assembly) |
A to T
at 37086011 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Arginine to Stop codon
at position 65
(R65*)
|
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 null
Transcript: ENSMUST00000115661
AA Change: R65*
|
SMART Domains |
Protein: ENSMUSP00000111325 Gene: ENSMUSG00000103458 AA Change: R65*
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 null
Transcript: ENSMUST00000192295
AA Change: R65*
|
SMART Domains |
Protein: ENSMUSP00000142103 Gene: ENSMUSG00000104252 AA Change: R65*
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 null
Transcript: ENSMUST00000192512
AA Change: R65*
|
SMART Domains |
Protein: ENSMUSP00000141408 Gene: ENSMUSG00000104252 AA Change: R65*
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 |
|
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: 55 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Acsl5 |
G |
A |
19: 55,266,523 (GRCm39) |
R114Q |
possibly damaging |
Het |
Atp1a4 |
C |
T |
1: 172,054,690 (GRCm39) |
V980I |
probably benign |
Het |
Bltp1 |
T |
A |
3: 37,013,007 (GRCm39) |
C1895S |
probably damaging |
Het |
Brd1 |
A |
T |
15: 88,614,729 (GRCm39) |
D55E |
probably benign |
Het |
Cachd1 |
A |
G |
4: 100,809,280 (GRCm39) |
D255G |
probably benign |
Het |
Ccdc168 |
A |
T |
1: 44,097,425 (GRCm39) |
D1224E |
possibly damaging |
Het |
Ces2f |
C |
A |
8: 105,676,704 (GRCm39) |
P133T |
probably damaging |
Het |
Cfap251 |
A |
T |
5: 123,460,505 (GRCm39) |
M1156L |
possibly damaging |
Het |
Clock |
GGCTGCTGCTGCTGCTGCTGCTGCTG |
GGCTGCTGCTGCTGCTGCTGCTG |
5: 76,374,889 (GRCm39) |
|
probably benign |
Het |
Cyp4f37 |
A |
T |
17: 32,844,096 (GRCm39) |
I67F |
probably benign |
Het |
Dbf4 |
T |
C |
5: 8,448,656 (GRCm39) |
I84V |
|
Het |
Dcc |
T |
C |
18: 71,511,755 (GRCm39) |
T887A |
probably benign |
Het |
Dhdh |
G |
T |
7: 45,137,536 (GRCm39) |
N50K |
probably benign |
Het |
Dnah7c |
A |
T |
1: 46,671,504 (GRCm39) |
E1631V |
probably damaging |
Het |
Dusp23 |
A |
G |
1: 172,460,293 (GRCm39) |
C53R |
possibly damaging |
Het |
Efcab6 |
G |
A |
15: 83,928,432 (GRCm39) |
S54L |
probably damaging |
Het |
Fcamr |
T |
C |
1: 130,739,335 (GRCm39) |
F212L |
probably damaging |
Het |
Gfap |
G |
C |
11: 102,787,810 (GRCm39) |
A45G |
probably benign |
Het |
Grm8 |
C |
T |
6: 27,363,752 (GRCm39) |
V588M |
probably benign |
Het |
H1f8 |
A |
G |
6: 115,926,911 (GRCm39) |
T263A |
probably benign |
Het |
Hoatz |
T |
A |
9: 50,992,832 (GRCm39) |
|
probably null |
Het |
Inhca |
T |
C |
9: 103,149,831 (GRCm39) |
Y242C |
probably damaging |
Het |
Malrd1 |
T |
A |
2: 15,570,368 (GRCm39) |
|
probably null |
Het |
Mxi1 |
G |
A |
19: 53,360,126 (GRCm39) |
G283S |
probably damaging |
Het |
Myh15 |
T |
C |
16: 48,997,366 (GRCm39) |
V1728A |
probably benign |
Het |
Nxph2 |
T |
A |
2: 23,290,071 (GRCm39) |
V141D |
probably damaging |
Het |
Or11l3 |
T |
C |
11: 58,515,994 (GRCm39) |
E106G |
unknown |
Het |
Or2t26 |
A |
T |
11: 49,039,483 (GRCm39) |
Y133F |
probably damaging |
Het |
Or4f6 |
A |
T |
2: 111,838,596 (GRCm39) |
S312T |
possibly damaging |
Het |
Or5b121 |
A |
T |
19: 13,507,892 (GRCm39) |
N329I |
probably damaging |
Het |
Or5d36 |
T |
A |
2: 87,901,753 (GRCm39) |
|
probably null |
Het |
Or5h25 |
A |
G |
16: 58,930,121 (GRCm39) |
V284A |
|
Het |
Or5w10 |
A |
T |
2: 87,375,753 (GRCm39) |
M45K |
probably damaging |
Het |
Or8c10 |
A |
G |
9: 38,279,142 (GRCm39) |
N90S |
possibly damaging |
Het |
Otof |
T |
A |
5: 30,578,325 (GRCm39) |
I108F |
probably benign |
Het |
Pde11a |
T |
C |
2: 76,041,434 (GRCm39) |
H412R |
probably benign |
Het |
Peli3 |
C |
T |
19: 4,982,541 (GRCm39) |
G375S |
probably damaging |
Het |
Ppp6r3 |
A |
G |
19: 3,561,927 (GRCm39) |
|
probably null |
Het |
Prcp |
T |
C |
7: 92,559,518 (GRCm39) |
V194A |
possibly damaging |
Het |
Prkce |
T |
C |
17: 86,476,370 (GRCm39) |
|
probably null |
Het |
Prss23 |
A |
T |
7: 89,159,887 (GRCm39) |
S61T |
probably benign |
Het |
Ptprq |
C |
T |
10: 107,535,469 (GRCm39) |
R432H |
probably damaging |
Het |
Rnase2a |
T |
A |
14: 51,493,101 (GRCm39) |
N88I |
possibly damaging |
Het |
Rspry1 |
G |
T |
8: 95,359,780 (GRCm39) |
L230F |
probably damaging |
Het |
Slco1a8 |
A |
G |
6: 141,927,810 (GRCm39) |
V548A |
probably damaging |
Het |
Smpd2 |
A |
G |
10: 41,365,301 (GRCm39) |
L65P |
probably benign |
Het |
Sorl1 |
A |
G |
9: 41,933,722 (GRCm39) |
Y1083H |
probably benign |
Het |
Tjp1 |
A |
G |
7: 64,986,386 (GRCm39) |
S241P |
probably damaging |
Het |
Tmed6 |
A |
C |
8: 107,792,164 (GRCm39) |
L27R |
probably damaging |
Het |
Tmem52 |
G |
A |
4: 155,553,788 (GRCm39) |
C32Y |
probably damaging |
Het |
Tmprss15 |
C |
A |
16: 78,750,834 (GRCm39) |
G1022* |
probably null |
Het |
Ttn |
T |
C |
2: 76,730,345 (GRCm39) |
S5085G |
unknown |
Het |
Vmn2r37 |
C |
T |
7: 9,209,854 (GRCm39) |
V553M |
possibly damaging |
Het |
Wdr70 |
A |
T |
15: 8,123,210 (GRCm39) |
M42K |
probably benign |
Het |
Zfp735 |
T |
A |
11: 73,602,510 (GRCm39) |
C485S |
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 |
|
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 |
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'- AATTCTCCTAGCTCTGAGAGAATC -3'
(R):5'- ACCTCCACGTGGAAAACCTG -3'
Sequencing Primer
(F):5'- GCACTGTGCACTTGAAATGG -3'
(R):5'- GGAAAACCTGCAACGGCCTG -3'
|
Posted On |
2021-07-15 |