Incidental Mutation 'R7950:Pcdha6'
|
List
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|
| ID | 649530 |
|---|
| Institutional Source |
Beutler Lab
|
|---|
| Gene Symbol |
Pcdha6
|
|---|
| Ensembl Gene |
ENSMUSG00000103707 |
|---|
| Gene Name | protocadherin alpha 6 |
|---|
| Synonyms | Crnr2, Cnr2 |
|---|
| MMRRC Submission |
|
|---|
| Accession Numbers | |
|---|
| Is this an essential gene? |
Probably non essential (E-score: 0.198)
|
|---|
| Stock # | R7950 (G1)
|
|---|
| Quality Score | 225.009 |
|---|
| Status |
Validated
|
|---|
| Chromosome | 18 |
|---|
| Chromosomal Location | 36967631-37187657 bp(+) (GRCm38) |
|---|
| Type of Mutation | missense |
|---|
| DNA Base Change (assembly) |
T to G
at 36969426 bp
|
|---|
| Zygosity | Heterozygous |
|---|
| Amino Acid Change |
Aspartic acid to Glutamic Acid
at position 557
(D557E)
|
|---|
| Ref Sequence |
ENSEMBL: ENSMUSP00000141587
(fasta)
|
|---|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000070797]
[ENSMUST00000115661]
[ENSMUST00000115662]
[ENSMUST00000192168]
[ENSMUST00000192295]
[ENSMUST00000192503]
[ENSMUST00000192512]
[ENSMUST00000192631]
[ENSMUST00000193389]
[ENSMUST00000193777]
[ENSMUST00000193839]
[ENSMUST00000194544]
[ENSMUST00000194751]
[ENSMUST00000195590]
|
|---|
| 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 benign
Transcript: ENSMUST00000115661
|
|---|
| SMART Domains |
Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458
| 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: ENSMUST00000192168
|
|---|
| SMART Domains |
Protein: ENSMUSP00000142293
Gene: ENSMUSG00000103092
| Domain | Start | End | E-Value | Type |
|---|
|
CA
|
21 |
131 |
2.2e-2 |
SMART |
|
CA
|
155 |
240 |
2.05e-21 |
SMART |
|
CA
|
264 |
348 |
8.81e-21 |
SMART |
|
CA
|
372 |
453 |
2.01e-24 |
SMART |
|
CA
|
477 |
563 |
1.42e-24 |
SMART |
|
CA
|
591 |
673 |
1.63e-15 |
SMART |
|
transmembrane domain
|
693 |
715 |
N/A |
INTRINSIC |
|
low complexity region
|
902 |
926 |
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 |
probably benign
Transcript: ENSMUST00000192512
|
|---|
| SMART Domains |
Protein: ENSMUSP00000141408
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 |
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: ENSMUST00000192631
|
|---|
| SMART Domains |
Protein: ENSMUSP00000142156
Gene: ENSMUSG00000104318
| Domain | Start | End | E-Value | Type |
|---|
|
CA
|
21 |
131 |
2.58e-2 |
SMART |
|
CA
|
155 |
240 |
4.27e-19 |
SMART |
|
CA
|
264 |
348 |
1.42e-24 |
SMART |
|
CA
|
372 |
453 |
9.36e-25 |
SMART |
|
CA
|
477 |
563 |
1.42e-24 |
SMART |
|
CA
|
594 |
671 |
4.03e-6 |
SMART |
|
transmembrane domain
|
696 |
718 |
N/A |
INTRINSIC |
|
low complexity region
|
905 |
929 |
N/A |
INTRINSIC |
|
|---|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000193389
AA Change: D557E
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
|---|
| SMART Domains |
Protein: ENSMUSP00000141459
Gene: ENSMUSG00000103707
AA Change: D557E
| Domain | Start | End | E-Value | Type |
|---|
|
CA
|
21 |
131 |
5.67e-2 |
SMART |
|
CA
|
155 |
240 |
4.72e-21 |
SMART |
|
CA
|
264 |
348 |
1.9e-25 |
SMART |
|
CA
|
372 |
453 |
3.31e-25 |
SMART |
|
CA
|
477 |
563 |
1.42e-24 |
SMART |
|
CA
|
594 |
676 |
5.91e-13 |
SMART |
|
|---|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000193777
AA Change: D557E
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
|---|
| SMART Domains |
Protein: ENSMUSP00000141587
Gene: ENSMUSG00000103707
AA Change: D557E
| Domain | Start | End | E-Value | Type |
|---|
|
CA
|
21 |
131 |
5.67e-2 |
SMART |
|
CA
|
155 |
240 |
4.72e-21 |
SMART |
|
CA
|
264 |
348 |
1.9e-25 |
SMART |
|
CA
|
372 |
453 |
3.31e-25 |
SMART |
|
CA
|
477 |
563 |
1.42e-24 |
SMART |
|
CA
|
594 |
676 |
5.91e-13 |
SMART |
|
low complexity region
|
914 |
938 |
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: ENSMUST00000194544
|
|---|
| SMART Domains |
Protein: ENSMUSP00000141847
Gene: ENSMUSG00000102836
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:CA
|
18 |
66 |
5e-20 |
BLAST |
|
|---|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000194751
|
|---|
| SMART Domains |
Protein: ENSMUSP00000142285
Gene: ENSMUSG00000103707
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
15 |
21 |
N/A |
INTRINSIC |
|
Pfam:Cadherin_2
|
29 |
112 |
4.5e-32 |
PFAM |
|
|---|
| 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: 99.7%
- 20x: 99.1%
|
|---|
| Validation Efficiency |
100% (47/47) |
|---|
| 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: 44 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1810043G02Rik |
C |
T |
10: 77,979,767 |
T31I |
probably damaging |
Het |
| Adgrf5 |
G |
A |
17: 43,451,157 |
V1248M |
probably damaging |
Het |
| Alb |
T |
C |
5: 90,472,464 |
S478P |
probably damaging |
Het |
| Arhgap17 |
A |
G |
7: 123,286,816 |
S698P |
probably benign |
Het |
| Arhgef5 |
A |
G |
6: 43,273,925 |
T537A |
possibly damaging |
Het |
| Arl6 |
A |
T |
16: 59,618,731 |
|
probably null |
Het |
| Atp13a4 |
A |
T |
16: 29,449,917 |
W540R |
|
Het |
| Birc6 |
A |
T |
17: 74,593,100 |
D1091V |
probably damaging |
Het |
| Bnc1 |
A |
G |
7: 81,973,502 |
V659A |
probably benign |
Het |
| C130074G19Rik |
T |
C |
1: 184,874,374 |
|
probably null |
Het |
| C1ql4 |
T |
A |
15: 99,084,812 |
H220L |
probably benign |
Het |
| Cacna1s |
A |
G |
1: 136,100,625 |
N1147S |
probably benign |
Het |
| Cc2d2a |
T |
C |
5: 43,695,296 |
|
probably null |
Het |
| Ccdc36 |
T |
C |
9: 108,405,671 |
T273A |
probably benign |
Het |
| Ccl1 |
T |
A |
11: 82,179,693 |
I18L |
probably benign |
Het |
| Ecel1 |
A |
T |
1: 87,148,269 |
Y729N |
probably damaging |
Het |
| Epha4 |
T |
A |
1: 77,507,196 |
I59F |
probably damaging |
Het |
| Filip1l |
A |
G |
16: 57,569,711 |
K221E |
probably damaging |
Het |
| Flnc |
A |
G |
6: 29,456,382 |
E2193G |
possibly damaging |
Het |
| Galnt10 |
C |
G |
11: 57,783,723 |
P513A |
probably damaging |
Het |
| Gm5624 |
A |
G |
14: 44,560,733 |
Y139H |
|
Het |
| Golgb1 |
A |
C |
16: 36,915,424 |
I1719L |
probably benign |
Het |
| Hsf1 |
T |
C |
15: 76,498,193 |
S255P |
probably benign |
Het |
| Ighv2-2 |
T |
C |
12: 113,588,294 |
D108G |
probably damaging |
Het |
| Kbtbd3 |
C |
T |
9: 4,316,878 |
Q10* |
probably null |
Het |
| Kcnh2 |
C |
T |
5: 24,333,036 |
V110M |
probably benign |
Het |
| Magi3 |
A |
C |
3: 104,016,689 |
L1112W |
probably damaging |
Het |
| Malrd1 |
T |
A |
2: 16,128,068 |
D1933E |
unknown |
Het |
| Mki67 |
G |
A |
7: 135,699,724 |
R1194* |
probably null |
Het |
| Nap1l1 |
T |
C |
10: 111,492,908 |
Y233H |
probably damaging |
Het |
| Napsa |
A |
G |
7: 44,585,334 |
I298V |
probably benign |
Het |
| Nkx6-1 |
A |
T |
5: 101,663,599 |
S212R |
probably damaging |
Het |
| Nlrc4 |
A |
T |
17: 74,445,615 |
I591N |
probably damaging |
Het |
| Olfr1468-ps1 |
T |
C |
19: 13,375,067 |
I35T |
possibly damaging |
Het |
| Orc2 |
T |
C |
1: 58,467,668 |
D503G |
possibly damaging |
Het |
| Osbp |
T |
A |
19: 11,978,248 |
S343T |
probably benign |
Het |
| Pdcd11 |
AGAGGAGGAGGAGGAGGAGGAGGAG |
AGAGGAGGAGGAGGAGGAGGAG |
19: 47,113,437 |
|
probably benign |
Het |
| Ppdpf |
A |
G |
2: 181,187,857 |
Y35C |
probably benign |
Het |
| Scrn2 |
T |
A |
11: 97,030,929 |
L75Q |
probably damaging |
Het |
| Scube3 |
G |
A |
17: 28,171,226 |
V955I |
probably benign |
Het |
| Slc1a1 |
T |
C |
19: 28,911,761 |
V478A |
probably benign |
Het |
| Slc4a4 |
A |
G |
5: 89,058,278 |
|
probably null |
Het |
| Srrm2 |
T |
C |
17: 23,808,110 |
L96P |
unknown |
Het |
| Strn |
A |
T |
17: 78,670,423 |
L175Q |
|
Het |
|
|---|
| Other mutations in Pcdha6 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
R3734:Pcdha6
|
UTSW |
18 |
36969401 |
missense |
probably damaging |
1.00 |
|
R3859:Pcdha6
|
UTSW |
18 |
36969931 |
missense |
possibly damaging |
0.89 |
|
R3875:Pcdha6
|
UTSW |
18 |
36968066 |
missense |
probably damaging |
1.00 |
|
R4446:Pcdha6
|
UTSW |
18 |
36967760 |
missense |
probably benign |
0.28 |
|
R4647:Pcdha6
|
UTSW |
18 |
36969136 |
missense |
probably damaging |
0.98 |
|
R4659:Pcdha6
|
UTSW |
18 |
36969239 |
missense |
probably damaging |
1.00 |
|
R4780:Pcdha6
|
UTSW |
18 |
36969853 |
missense |
probably damaging |
1.00 |
|
R4839:Pcdha6
|
UTSW |
18 |
36968432 |
missense |
possibly damaging |
0.73 |
|
R4915:Pcdha6
|
UTSW |
18 |
36968457 |
missense |
probably damaging |
1.00 |
|
R5011:Pcdha6
|
UTSW |
18 |
36967907 |
missense |
probably damaging |
1.00 |
|
R5084:Pcdha6
|
UTSW |
18 |
36968963 |
missense |
probably damaging |
1.00 |
|
R5090:Pcdha6
|
UTSW |
18 |
36968717 |
missense |
probably benign |
0.15 |
|
R5189:Pcdha6
|
UTSW |
18 |
36968791 |
missense |
probably damaging |
1.00 |
|
R5652:Pcdha6
|
UTSW |
18 |
36968836 |
splice site |
probably null |
|
|
R5773:Pcdha6
|
UTSW |
18 |
36969590 |
missense |
probably benign |
0.00 |
|
R5890:Pcdha6
|
UTSW |
18 |
36969068 |
missense |
possibly damaging |
0.94 |
|
R6135:Pcdha6
|
UTSW |
18 |
36969216 |
missense |
probably damaging |
1.00 |
|
R6276:Pcdha6
|
UTSW |
18 |
36969767 |
splice site |
probably null |
|
|
R6346:Pcdha6
|
UTSW |
18 |
36968060 |
missense |
probably damaging |
1.00 |
|
R6889:Pcdha6
|
UTSW |
18 |
36968343 |
missense |
probably damaging |
1.00 |
|
R7295:Pcdha6
|
UTSW |
18 |
36968136 |
missense |
probably damaging |
1.00 |
|
R7776:Pcdha6
|
UTSW |
18 |
36969981 |
missense |
probably benign |
0.27 |
|
R7944:Pcdha6
|
UTSW |
18 |
36968912 |
missense |
possibly damaging |
0.55 |
|
R8371:Pcdha6
|
UTSW |
18 |
36969867 |
nonsense |
probably null |
|
|
R8513:Pcdha6
|
UTSW |
18 |
36969176 |
missense |
probably damaging |
1.00 |
|
R8549:Pcdha6
|
UTSW |
18 |
36968541 |
missense |
possibly damaging |
0.83 |
|
Z1088:Pcdha6
|
UTSW |
18 |
36969217 |
missense |
probably damaging |
1.00 |
|
|---|
| Predicted Primers |
PCR Primer
(F):5'- CTTCACAGTATCGGCGATGGAC -3'
(R):5'- AGGATGCAGCTCATAAGACAGC -3'
Sequencing Primer
(F):5'- AACGCGCTGGTGTCCTACTC -3'
(R):5'- GCTCATAAGACAGCCAGGCATTATAG -3'
|
|---|
| Posted On | 2020-09-15 |
|---|
