Incidental Mutation 'R4493:Pcdha4'
ID |
330850 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Pcdha4
|
Ensembl Gene |
ENSMUSG00000104252 |
Gene Name |
protocadherin alpha 4 |
Synonyms |
Crnr1, Cnr1 |
MMRRC Submission |
041748-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.161)
|
Stock # |
R4493 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
18 |
Chromosomal Location |
37085742-37320710 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 37087644 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Tyrosine to Phenylalanine
at position 609
(Y609F)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000141408
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000070797]
[ENSMUST00000115661]
[ENSMUST00000115662]
[ENSMUST00000192295]
[ENSMUST00000192503]
[ENSMUST00000192512]
[ENSMUST00000195590]
[ENSMUST00000193839]
|
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 |
possibly damaging
Transcript: ENSMUST00000115661
AA Change: Y609F
PolyPhen 2
Score 0.803 (Sensitivity: 0.84; Specificity: 0.93)
|
SMART Domains |
Protein: ENSMUSP00000111325 Gene: ENSMUSG00000103458 AA Change: Y609F
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 |
possibly damaging
Transcript: ENSMUST00000192512
AA Change: Y609F
PolyPhen 2
Score 0.803 (Sensitivity: 0.84; Specificity: 0.93)
|
SMART Domains |
Protein: ENSMUSP00000141408 Gene: ENSMUSG00000104252 AA Change: Y609F
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 |
noncoding transcript
Transcript: ENSMUST00000194235
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000194001
|
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 |
|
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 |
|
Meta Mutation Damage Score |
0.4197 |
Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.7%
|
Validation Efficiency |
94% (45/48) |
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: 40 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Cacna1b |
T |
C |
2: 24,542,950 (GRCm39) |
T1301A |
probably damaging |
Het |
Ccdc141 |
A |
G |
2: 76,962,641 (GRCm39) |
V101A |
probably damaging |
Het |
Ccdc146 |
T |
C |
5: 21,508,191 (GRCm39) |
E619G |
possibly damaging |
Het |
Cfap91 |
T |
C |
16: 38,162,130 (GRCm39) |
T4A |
probably benign |
Het |
Cmya5 |
T |
C |
13: 93,230,573 (GRCm39) |
E1505G |
probably benign |
Het |
Cngb3 |
C |
A |
4: 19,367,778 (GRCm39) |
P229Q |
probably damaging |
Het |
Ctnna2 |
A |
G |
6: 76,958,831 (GRCm39) |
V461A |
probably damaging |
Het |
D430041D05Rik |
T |
C |
2: 104,086,684 (GRCm39) |
D764G |
probably benign |
Het |
Dgki |
T |
C |
6: 36,951,796 (GRCm39) |
|
probably benign |
Het |
Dhx36 |
A |
T |
3: 62,395,925 (GRCm39) |
|
probably benign |
Het |
Gcn1 |
T |
C |
5: 115,732,203 (GRCm39) |
I1006T |
probably benign |
Het |
Glt8d2 |
T |
A |
10: 82,500,547 (GRCm39) |
M20L |
possibly damaging |
Het |
Greb1 |
C |
A |
12: 16,748,611 (GRCm39) |
G1122V |
probably benign |
Het |
Hmcn1 |
A |
T |
1: 150,577,650 (GRCm39) |
I2037N |
probably damaging |
Het |
Hspa4l |
A |
G |
3: 40,722,434 (GRCm39) |
I340V |
possibly damaging |
Het |
Itpr3 |
A |
G |
17: 27,323,586 (GRCm39) |
K1204E |
probably damaging |
Het |
Kcnh8 |
GAGACCAACGAGCAGCTGATGCTTCAGA |
GAGA |
17: 53,032,934 (GRCm39) |
74 |
probably benign |
Het |
Lyst |
G |
A |
13: 13,809,968 (GRCm39) |
R546H |
probably damaging |
Het |
Mcph1 |
T |
A |
8: 18,681,752 (GRCm39) |
C296* |
probably null |
Het |
Mrc2 |
G |
A |
11: 105,239,257 (GRCm39) |
|
probably null |
Het |
Naga |
A |
G |
15: 82,216,715 (GRCm39) |
F259S |
probably damaging |
Het |
Nes |
A |
G |
3: 87,884,120 (GRCm39) |
E793G |
probably damaging |
Het |
Nfkb2 |
A |
G |
19: 46,296,878 (GRCm39) |
D316G |
probably damaging |
Het |
Pgam1 |
C |
T |
19: 41,904,215 (GRCm39) |
A104V |
possibly damaging |
Het |
Piezo2 |
T |
C |
18: 63,247,134 (GRCm39) |
I525V |
probably damaging |
Het |
Pold1 |
A |
G |
7: 44,187,132 (GRCm39) |
V683A |
probably damaging |
Het |
Poteg |
T |
C |
8: 27,970,125 (GRCm39) |
V316A |
possibly damaging |
Het |
Ppih |
A |
T |
4: 119,168,042 (GRCm39) |
N156K |
probably damaging |
Het |
Prep |
T |
C |
10: 44,996,915 (GRCm39) |
F398L |
probably benign |
Het |
Prlhr |
A |
T |
19: 60,455,519 (GRCm39) |
M349K |
probably benign |
Het |
Rtp4 |
A |
T |
16: 23,428,827 (GRCm39) |
H30L |
probably benign |
Het |
Stkld1 |
A |
G |
2: 26,836,638 (GRCm39) |
N268S |
probably benign |
Het |
Syt6 |
A |
G |
3: 103,492,946 (GRCm39) |
E66G |
probably damaging |
Het |
Tas2r129 |
A |
G |
6: 132,928,317 (GRCm39) |
I85V |
probably benign |
Het |
Tma16 |
C |
T |
8: 66,936,823 (GRCm39) |
|
probably null |
Het |
Tprn |
T |
C |
2: 25,158,904 (GRCm39) |
S643P |
probably damaging |
Het |
Trrap |
T |
C |
5: 144,767,858 (GRCm39) |
V2605A |
probably benign |
Het |
Vmn1r230 |
T |
A |
17: 21,066,863 (GRCm39) |
N17K |
probably benign |
Het |
Xkrx |
T |
C |
X: 133,051,745 (GRCm39) |
N302S |
possibly damaging |
Het |
Zfp946 |
T |
A |
17: 22,670,067 (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 |
|
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'- GCAATGTGACTCTGCAGGTG -3'
(R):5'- TACTCGCGATGGAGCCTTTG -3'
Sequencing Primer
(F):5'- GTTTGTGCTGGACGAGAATGACAAC -3'
(R):5'- CGATGGAGCCTTTGGTACC -3'
|
Posted On |
2015-07-21 |