Incidental Mutation 'R4827:Pcdha4'
| ID |
372531 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha4
|
| Ensembl Gene |
ENSMUSG00000104252 |
| Gene Name |
protocadherin alpha 4 |
| Synonyms |
Crnr1, Cnr1 |
| MMRRC Submission |
042443-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.161)
|
| Stock # |
R4827 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
37085742-37320710 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 37086251 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Proline
at position 145
(S145P)
|
| 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: S145P
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458
AA Change: S145P
| 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: S145P
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000142103
Gene: ENSMUSG00000104252
AA Change: S145P
| 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: S145P
PolyPhen 2
Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000141408
Gene: ENSMUSG00000104252
AA Change: S145P
| 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: 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 |
|
| Meta Mutation Damage Score |
0.6000 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 94.0%
|
| Validation Efficiency |
96% (67/70) |
| 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: 67 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adck1 |
A |
G |
12: 88,413,489 (GRCm39) |
R274G |
probably benign |
Het |
| Agbl5 |
T |
G |
5: 31,053,158 (GRCm39) |
S83R |
probably damaging |
Het |
| Ankib1 |
A |
G |
5: 3,751,907 (GRCm39) |
I711T |
probably damaging |
Het |
| Arnt |
T |
A |
3: 95,397,224 (GRCm39) |
|
probably null |
Het |
| Atad2 |
C |
G |
15: 57,971,744 (GRCm39) |
V702L |
probably benign |
Het |
| B4galnt4 |
A |
G |
7: 140,648,392 (GRCm39) |
E636G |
probably benign |
Het |
| Btbd2 |
A |
G |
10: 80,482,223 (GRCm39) |
I244T |
probably damaging |
Het |
| Cenpc1 |
A |
T |
5: 86,182,290 (GRCm39) |
N531K |
possibly damaging |
Het |
| Ces3b |
T |
A |
8: 105,813,527 (GRCm39) |
M266K |
probably benign |
Het |
| Cfap54 |
A |
T |
10: 92,737,937 (GRCm39) |
|
probably benign |
Het |
| Coq8a |
A |
G |
1: 179,994,903 (GRCm39) |
V590A |
possibly damaging |
Het |
| Drc7 |
A |
G |
8: 95,798,267 (GRCm39) |
Y504C |
probably damaging |
Het |
| Elovl4 |
T |
C |
9: 83,688,091 (GRCm39) |
M1V |
probably null |
Het |
| Exd1 |
C |
T |
2: 119,350,807 (GRCm39) |
A485T |
probably benign |
Het |
| Fads2 |
A |
G |
19: 10,059,958 (GRCm39) |
F239L |
probably benign |
Het |
| Gcc2 |
A |
T |
10: 58,121,953 (GRCm39) |
|
probably null |
Het |
| Ggact |
C |
T |
14: 123,128,987 (GRCm39) |
R76H |
probably benign |
Het |
| Gm17535 |
T |
A |
9: 3,035,786 (GRCm39) |
L218H |
probably benign |
Het |
| Gm3739 |
A |
T |
14: 18,506,218 (GRCm39) |
F13I |
probably damaging |
Het |
| Gng2 |
T |
C |
14: 19,925,898 (GRCm39) |
K65E |
possibly damaging |
Het |
| Gnmt |
A |
G |
17: 47,038,245 (GRCm39) |
Y94H |
possibly damaging |
Het |
| Gzme |
C |
A |
14: 56,356,755 (GRCm39) |
R69M |
probably null |
Het |
| Hdc |
G |
A |
2: 126,436,233 (GRCm39) |
P546L |
probably benign |
Het |
| Ibtk |
C |
A |
9: 85,610,607 (GRCm39) |
V326F |
probably benign |
Het |
| Inpp5b |
G |
T |
4: 124,637,643 (GRCm39) |
|
probably benign |
Het |
| Kcnh7 |
A |
T |
2: 62,546,564 (GRCm39) |
C1006S |
probably benign |
Het |
| Kcnk18 |
A |
T |
19: 59,208,362 (GRCm39) |
N66I |
probably damaging |
Het |
| Lpar6 |
T |
A |
14: 73,476,190 (GRCm39) |
N50K |
probably damaging |
Het |
| Lrba |
G |
T |
3: 86,267,457 (GRCm39) |
D1716Y |
possibly damaging |
Het |
| Ltf |
T |
A |
9: 110,856,445 (GRCm39) |
|
probably benign |
Het |
| Map3k6 |
A |
G |
4: 132,976,160 (GRCm39) |
T794A |
possibly damaging |
Het |
| Mcm8 |
A |
G |
2: 132,665,174 (GRCm39) |
T217A |
probably damaging |
Het |
| Meaf6 |
A |
G |
4: 124,996,713 (GRCm39) |
E141G |
probably damaging |
Het |
| Mmp13 |
A |
G |
9: 7,278,880 (GRCm39) |
T324A |
possibly damaging |
Het |
| Mplkipl1 |
C |
T |
19: 61,164,364 (GRCm39) |
G24R |
unknown |
Het |
| Msl2 |
T |
G |
9: 100,979,350 (GRCm39) |
F575V |
probably benign |
Het |
| Ncoa4-ps |
C |
T |
12: 119,225,529 (GRCm39) |
|
noncoding transcript |
Het |
| Nlrp2 |
A |
T |
7: 5,331,950 (GRCm39) |
W149R |
possibly damaging |
Het |
| Ntng1 |
C |
A |
3: 110,042,727 (GRCm39) |
C33F |
probably damaging |
Het |
| Nxn |
A |
G |
11: 76,152,418 (GRCm39) |
Y359H |
probably benign |
Het |
| Olfml2a |
A |
C |
2: 38,850,033 (GRCm39) |
D583A |
probably damaging |
Het |
| Or12j5 |
A |
C |
7: 140,083,583 (GRCm39) |
L263R |
probably damaging |
Het |
| Or1e32 |
A |
T |
11: 73,705,547 (GRCm39) |
Y120* |
probably null |
Het |
| Or2t48 |
A |
G |
11: 58,420,422 (GRCm39) |
I130T |
probably damaging |
Het |
| Or4b1b |
A |
T |
2: 90,112,547 (GRCm39) |
I124N |
probably damaging |
Het |
| Or51ac3 |
A |
T |
7: 103,213,752 (GRCm39) |
S245T |
probably damaging |
Het |
| Pcsk2 |
A |
T |
2: 143,643,099 (GRCm39) |
K459* |
probably null |
Het |
| Pirb |
C |
T |
7: 3,720,602 (GRCm39) |
G299S |
probably benign |
Het |
| Plch2 |
A |
G |
4: 155,075,570 (GRCm39) |
F653S |
probably damaging |
Het |
| Plpp3 |
T |
C |
4: 105,088,167 (GRCm39) |
I296T |
probably benign |
Het |
| Polr2b |
A |
G |
5: 77,490,398 (GRCm39) |
E846G |
probably benign |
Het |
| Ptpro |
A |
T |
6: 137,419,708 (GRCm39) |
N157Y |
probably damaging |
Het |
| Ralgapa1 |
A |
G |
12: 55,723,222 (GRCm39) |
L1815P |
probably damaging |
Het |
| Sap18 |
A |
G |
14: 58,036,020 (GRCm39) |
N69D |
probably damaging |
Het |
| Sncg |
C |
A |
14: 34,095,284 (GRCm39) |
V74F |
probably damaging |
Het |
| Spata31e2 |
T |
C |
1: 26,724,923 (GRCm39) |
K86E |
possibly damaging |
Het |
| Spmip4 |
A |
C |
6: 50,572,836 (GRCm39) |
S26A |
possibly damaging |
Het |
| Tmem186 |
A |
T |
16: 8,453,681 (GRCm39) |
Y193* |
probably null |
Het |
| Trrap |
A |
G |
5: 144,737,758 (GRCm39) |
S1045G |
probably benign |
Het |
| Tti2 |
T |
G |
8: 31,640,998 (GRCm39) |
S41A |
probably benign |
Het |
| Unc13c |
T |
C |
9: 73,838,568 (GRCm39) |
E761G |
probably damaging |
Het |
| Vamp2 |
T |
A |
11: 68,980,637 (GRCm39) |
D68E |
probably benign |
Het |
| Vmn1r200 |
A |
T |
13: 22,579,265 (GRCm39) |
M14L |
probably benign |
Het |
| Vps35 |
T |
A |
8: 86,000,186 (GRCm39) |
D480V |
possibly damaging |
Het |
| Zfp462 |
T |
C |
4: 55,012,213 (GRCm39) |
L1393P |
probably damaging |
Het |
| Zfp512 |
G |
A |
5: 31,630,158 (GRCm39) |
M274I |
probably benign |
Het |
| Znfx1 |
C |
G |
2: 166,886,151 (GRCm39) |
G803A |
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 |
|
|
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'- TTGTGAATTCTCGGATCGACC -3'
(R):5'- TTCCTCCGTCCGTGACAGTAAG -3'
Sequencing Primer
(F):5'- CGGGAGGAGCTGTGCGG -3'
(R):5'- GAGTTTCCTCCCGGTCTAAAG -3'
|
| Posted On |
2016-03-01 |
Incidental Mutation