Incidental Mutation 'R5090:Pcdha6'
| ID |
387724 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha6
|
| Ensembl Gene |
ENSMUSG00000103707 |
| Gene Name |
protocadherin alpha 6 |
| Synonyms |
Cnr2, Crnr2 |
| MMRRC Submission |
042679-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.156)
|
| Stock # |
R5090 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
37100684-37320710 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 37101770 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Valine
at position 321
(D321V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000141587
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000070797]
[ENSMUST00000115661]
[ENSMUST00000115662]
[ENSMUST00000192168]
[ENSMUST00000192295]
[ENSMUST00000192503]
[ENSMUST00000193389]
[ENSMUST00000193777]
[ENSMUST00000195590]
[ENSMUST00000193839]
[ENSMUST00000192512]
[ENSMUST00000194751]
[ENSMUST00000194544]
|
| AlphaFold |
Q91Y14 |
| 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 |
noncoding transcript
Transcript: ENSMUST00000192178
|
| 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: ENSMUST00000193389
AA Change: D321V
PolyPhen 2
Score 0.122 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000141459
Gene: ENSMUSG00000103707
AA Change: D321V
| 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 benign
Transcript: ENSMUST00000193777
AA Change: D321V
PolyPhen 2
Score 0.147 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000141587
Gene: ENSMUSG00000103707
AA Change: D321V
| 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: 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 |
|
| 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: 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: ENSMUST00000194544
|
| SMART Domains |
Protein: ENSMUSP00000141847
Gene: ENSMUSG00000102836
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:CA
|
18 |
66 |
5e-20 |
BLAST |
|
| Meta Mutation Damage Score |
0.4363 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.3%
- 10x: 96.3%
- 20x: 92.2%
|
| Validation Efficiency |
99% (66/67) |
| 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: 60 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca15 |
A |
G |
7: 119,984,422 (GRCm39) |
S1168G |
probably damaging |
Het |
| Acsf2 |
A |
T |
11: 94,462,095 (GRCm39) |
|
probably null |
Het |
| Ankk1 |
G |
T |
9: 49,333,063 (GRCm39) |
S140R |
probably damaging |
Het |
| Ash1l |
G |
T |
3: 88,960,184 (GRCm39) |
K2305N |
probably damaging |
Het |
| Asnsd1 |
C |
T |
1: 53,391,563 (GRCm39) |
|
probably benign |
Het |
| Atxn7l1 |
T |
C |
12: 33,376,077 (GRCm39) |
S51P |
probably damaging |
Het |
| Ccdc88c |
A |
G |
12: 100,920,439 (GRCm39) |
L394P |
probably damaging |
Het |
| Cd200r1 |
T |
A |
16: 44,609,924 (GRCm39) |
S48T |
possibly damaging |
Het |
| Cemip |
T |
C |
7: 83,591,343 (GRCm39) |
E1243G |
probably damaging |
Het |
| Cep192 |
T |
A |
18: 67,993,617 (GRCm39) |
H1977Q |
possibly damaging |
Het |
| Cep250 |
T |
C |
2: 155,818,324 (GRCm39) |
L833P |
probably damaging |
Het |
| Chd9 |
C |
A |
8: 91,753,462 (GRCm39) |
Y1818* |
probably null |
Het |
| Clca3a1 |
C |
A |
3: 144,443,633 (GRCm39) |
V706L |
probably benign |
Het |
| Cntln |
T |
C |
4: 84,865,830 (GRCm39) |
V162A |
probably damaging |
Het |
| Col5a1 |
G |
A |
2: 27,908,614 (GRCm39) |
W67* |
probably null |
Het |
| Cux1 |
T |
A |
5: 136,342,054 (GRCm39) |
N446I |
possibly damaging |
Het |
| Dlg1 |
G |
T |
16: 31,656,902 (GRCm39) |
G599W |
probably damaging |
Het |
| Dock7 |
C |
T |
4: 98,879,648 (GRCm39) |
V969I |
probably benign |
Het |
| Ephb3 |
T |
C |
16: 21,033,237 (GRCm39) |
C74R |
probably damaging |
Het |
| Fads6 |
T |
A |
11: 115,187,480 (GRCm39) |
T72S |
probably benign |
Het |
| Fra10ac1 |
C |
T |
19: 38,202,873 (GRCm39) |
R110Q |
probably damaging |
Het |
| Gdf3 |
T |
A |
6: 122,586,713 (GRCm39) |
L71F |
probably benign |
Het |
| Gm6685 |
A |
G |
11: 28,289,253 (GRCm39) |
Y188H |
probably benign |
Het |
| Gm6981 |
A |
C |
9: 51,914,142 (GRCm39) |
|
noncoding transcript |
Het |
| Gnpda1 |
T |
C |
18: 38,465,146 (GRCm39) |
T157A |
probably damaging |
Het |
| Grap2 |
A |
C |
15: 80,522,683 (GRCm39) |
N70H |
possibly damaging |
Het |
| Gvin3 |
T |
A |
7: 106,200,109 (GRCm39) |
|
noncoding transcript |
Het |
| Hdac5 |
G |
A |
11: 102,088,539 (GRCm39) |
R887C |
probably damaging |
Het |
| Hectd3 |
T |
A |
4: 116,857,435 (GRCm39) |
|
probably benign |
Het |
| Hmgcr |
T |
C |
13: 96,787,098 (GRCm39) |
K162E |
probably benign |
Het |
| Inpp5e |
A |
T |
2: 26,289,383 (GRCm39) |
|
probably null |
Het |
| Kifap3 |
A |
G |
1: 163,683,645 (GRCm39) |
D442G |
possibly damaging |
Het |
| Lama3 |
A |
G |
18: 12,675,459 (GRCm39) |
T1015A |
possibly damaging |
Het |
| Lcp2 |
T |
A |
11: 34,039,725 (GRCm39) |
Y508* |
probably null |
Het |
| Map1b |
G |
T |
13: 99,566,534 (GRCm39) |
Y2062* |
probably null |
Het |
| Mipep |
A |
G |
14: 61,039,748 (GRCm39) |
D259G |
possibly damaging |
Het |
| Mmp2 |
T |
C |
8: 93,579,202 (GRCm39) |
F97S |
probably damaging |
Het |
| Mrpl18 |
A |
C |
17: 13,132,697 (GRCm39) |
M144R |
probably damaging |
Het |
| Nek9 |
A |
G |
12: 85,376,616 (GRCm39) |
|
probably null |
Het |
| Nmral1 |
A |
T |
16: 4,532,395 (GRCm39) |
Y139N |
probably damaging |
Het |
| Notch4 |
T |
C |
17: 34,799,894 (GRCm39) |
C952R |
probably damaging |
Het |
| Nsf |
T |
C |
11: 103,801,404 (GRCm39) |
N204D |
probably benign |
Het |
| P2rx4 |
A |
T |
5: 122,863,118 (GRCm39) |
D197V |
probably damaging |
Het |
| Pak5 |
A |
T |
2: 135,929,338 (GRCm39) |
I615N |
probably damaging |
Het |
| Parp10 |
T |
C |
15: 76,125,925 (GRCm39) |
D421G |
probably damaging |
Het |
| Pkhd1 |
T |
A |
1: 20,270,981 (GRCm39) |
I3191F |
probably damaging |
Het |
| Psmd4 |
T |
C |
3: 94,942,559 (GRCm39) |
N7S |
possibly damaging |
Het |
| Ptprq |
A |
G |
10: 107,361,950 (GRCm39) |
V2084A |
probably damaging |
Het |
| Rab3gap1 |
A |
G |
1: 127,843,415 (GRCm39) |
E263G |
probably benign |
Het |
| Rbm5 |
A |
G |
9: 107,637,511 (GRCm39) |
|
probably benign |
Het |
| Sacs |
T |
C |
14: 61,442,702 (GRCm39) |
F1583L |
probably damaging |
Het |
| Sel1l3 |
G |
T |
5: 53,357,388 (GRCm39) |
H201Q |
probably benign |
Het |
| Shoc1 |
T |
C |
4: 59,111,108 (GRCm39) |
T55A |
unknown |
Het |
| Tdpoz3 |
T |
A |
3: 93,733,870 (GRCm39) |
W182R |
possibly damaging |
Het |
| Trim55 |
A |
G |
3: 19,725,771 (GRCm39) |
N313S |
probably benign |
Het |
| Usp17lb |
A |
T |
7: 104,490,290 (GRCm39) |
D212E |
probably benign |
Het |
| Xirp2 |
A |
G |
2: 67,355,814 (GRCm39) |
E3525G |
possibly damaging |
Het |
| Zfp236 |
T |
C |
18: 82,637,006 (GRCm39) |
T1379A |
probably benign |
Het |
| Zfp553 |
A |
T |
7: 126,834,659 (GRCm39) |
E71D |
probably damaging |
Het |
| Znrf1 |
T |
G |
8: 112,265,035 (GRCm39) |
F21V |
probably benign |
Het |
|
| Other mutations in Pcdha6 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
R3734:Pcdha6
|
UTSW |
18 |
37,102,454 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3859:Pcdha6
|
UTSW |
18 |
37,102,984 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R3875:Pcdha6
|
UTSW |
18 |
37,101,119 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4446:Pcdha6
|
UTSW |
18 |
37,100,813 (GRCm39) |
missense |
probably benign |
0.28 |
|
R4647:Pcdha6
|
UTSW |
18 |
37,102,189 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4659:Pcdha6
|
UTSW |
18 |
37,102,292 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4780:Pcdha6
|
UTSW |
18 |
37,102,906 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4839:Pcdha6
|
UTSW |
18 |
37,101,485 (GRCm39) |
missense |
possibly damaging |
0.73 |
|
R4915:Pcdha6
|
UTSW |
18 |
37,101,510 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5011:Pcdha6
|
UTSW |
18 |
37,100,960 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5084:Pcdha6
|
UTSW |
18 |
37,102,016 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5189:Pcdha6
|
UTSW |
18 |
37,101,844 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5652:Pcdha6
|
UTSW |
18 |
37,101,889 (GRCm39) |
splice site |
probably null |
|
|
R5773:Pcdha6
|
UTSW |
18 |
37,102,643 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5890:Pcdha6
|
UTSW |
18 |
37,102,121 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R6135:Pcdha6
|
UTSW |
18 |
37,102,269 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6276:Pcdha6
|
UTSW |
18 |
37,102,820 (GRCm39) |
splice site |
probably null |
|
|
R6346:Pcdha6
|
UTSW |
18 |
37,101,113 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6889:Pcdha6
|
UTSW |
18 |
37,101,396 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7295:Pcdha6
|
UTSW |
18 |
37,101,189 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7776:Pcdha6
|
UTSW |
18 |
37,103,034 (GRCm39) |
missense |
probably benign |
0.27 |
|
R7944:Pcdha6
|
UTSW |
18 |
37,101,965 (GRCm39) |
missense |
possibly damaging |
0.55 |
|
R7950:Pcdha6
|
UTSW |
18 |
37,102,479 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8371:Pcdha6
|
UTSW |
18 |
37,102,920 (GRCm39) |
nonsense |
probably null |
|
|
R8513:Pcdha6
|
UTSW |
18 |
37,102,229 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8549:Pcdha6
|
UTSW |
18 |
37,101,594 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
R8735:Pcdha6
|
UTSW |
18 |
37,101,203 (GRCm39) |
missense |
possibly damaging |
0.55 |
|
R8827:Pcdha6
|
UTSW |
18 |
37,102,802 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8881:Pcdha6
|
UTSW |
18 |
37,101,484 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9094:Pcdha6
|
UTSW |
18 |
37,101,593 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R9357:Pcdha6
|
UTSW |
18 |
37,102,226 (GRCm39) |
missense |
probably benign |
0.16 |
|
Z1088:Pcdha6
|
UTSW |
18 |
37,102,270 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- ATGCTTCTGACAAGGATGAAGG -3'
(R):5'- ACACCAACTTGAAGGGGACATG -3'
Sequencing Primer
(F):5'- GGGACGAATTCAGCAATTTCGTACTC -3'
(R):5'- TTGGATCCAGAGTCCAGATCC -3'
|
| Posted On |
2016-06-06 |
Incidental Mutation