Incidental Mutation 'R7295:Pcdha6'
| ID |
566702 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha6
|
| Ensembl Gene |
ENSMUSG00000103707 |
| Gene Name |
protocadherin alpha 6 |
| Synonyms |
Cnr2, Crnr2 |
| MMRRC Submission |
045363-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.172)
|
| Stock # |
R7295 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
37100684-37320710 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 37101189 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Lysine
at position 127
(N127K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000141587
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000070797]
[ENSMUST00000115661]
[ENSMUST00000115662]
[ENSMUST00000192168]
[ENSMUST00000192295]
[ENSMUST00000192503]
[ENSMUST00000192512]
[ENSMUST00000193777]
[ENSMUST00000193389]
[ENSMUST00000193839]
[ENSMUST00000194544]
[ENSMUST00000194751]
[ENSMUST00000195590]
|
| 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 |
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 damaging
Transcript: ENSMUST00000193777
AA Change: N127K
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000141587
Gene: ENSMUSG00000103707
AA Change: N127K
| 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 damaging
Transcript: ENSMUST00000193389
AA Change: N127K
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000141459
Gene: ENSMUSG00000103707
AA Change: N127K
| 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: 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 |
|
| Meta Mutation Damage Score |
0.6467 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.3%
|
| Validation Efficiency |
98% (59/60) |
| 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: 61 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| a |
A |
T |
2: 154,887,678 (GRCm39) |
D46V |
probably damaging |
Het |
| Acp7 |
A |
T |
7: 28,328,955 (GRCm39) |
F75Y |
possibly damaging |
Het |
| Adamts19 |
T |
A |
18: 58,970,955 (GRCm39) |
Y180N |
probably damaging |
Het |
| Adck1 |
G |
T |
12: 88,397,815 (GRCm39) |
D150Y |
probably damaging |
Het |
| Alb |
T |
A |
5: 90,610,693 (GRCm39) |
|
probably null |
Het |
| Baat |
A |
T |
4: 49,490,275 (GRCm39) |
Y270N |
probably damaging |
Het |
| Bmp7 |
A |
T |
2: 172,781,690 (GRCm39) |
I58N |
probably damaging |
Het |
| Bpifb9a |
C |
T |
2: 154,109,616 (GRCm39) |
T504M |
probably damaging |
Het |
| Cbfa2t3 |
T |
G |
8: 123,364,768 (GRCm39) |
D338A |
probably benign |
Het |
| Ccnd2 |
A |
T |
6: 127,125,725 (GRCm39) |
C104S |
possibly damaging |
Het |
| Clip1 |
G |
T |
5: 123,765,419 (GRCm39) |
Q713K |
probably benign |
Het |
| Ddx28 |
G |
A |
8: 106,737,476 (GRCm39) |
S194L |
probably benign |
Het |
| Dync1h1 |
T |
C |
12: 110,631,183 (GRCm39) |
|
probably null |
Het |
| Edil3 |
T |
A |
13: 89,279,902 (GRCm39) |
Y193* |
probably null |
Het |
| Eprs1 |
A |
G |
1: 185,150,407 (GRCm39) |
|
probably null |
Het |
| Ercc6l2 |
T |
G |
13: 63,967,589 (GRCm39) |
I63R |
probably damaging |
Het |
| Fam171a2 |
T |
C |
11: 102,329,064 (GRCm39) |
E565G |
possibly damaging |
Het |
| Fbn1 |
T |
A |
2: 125,177,407 (GRCm39) |
D1810V |
probably damaging |
Het |
| Foxj2 |
T |
C |
6: 122,817,190 (GRCm39) |
S506P |
probably benign |
Het |
| Frmpd1 |
A |
G |
4: 45,285,700 (GRCm39) |
E1507G |
probably damaging |
Het |
| Gfm1 |
G |
A |
3: 67,347,514 (GRCm39) |
V258I |
probably benign |
Het |
| Gphn |
T |
C |
12: 78,538,876 (GRCm39) |
V174A |
probably benign |
Het |
| Gtpbp3 |
C |
A |
8: 71,942,139 (GRCm39) |
S123R |
possibly damaging |
Het |
| H2bc8 |
T |
C |
13: 23,755,943 (GRCm39) |
S113P |
probably benign |
Het |
| Hbs1l |
T |
C |
10: 21,186,051 (GRCm39) |
V491A |
probably benign |
Het |
| Hoxc12 |
A |
G |
15: 102,846,810 (GRCm39) |
N234S |
probably damaging |
Het |
| Il22b |
A |
T |
10: 118,130,848 (GRCm39) |
L16* |
probably null |
Het |
| Kcnj5 |
T |
C |
9: 32,234,087 (GRCm39) |
D76G |
probably damaging |
Het |
| Klhl11 |
A |
G |
11: 100,363,068 (GRCm39) |
Y163H |
probably damaging |
Het |
| Lonp1 |
G |
T |
17: 56,929,495 (GRCm39) |
Q181K |
possibly damaging |
Het |
| Mgst1 |
A |
T |
6: 138,124,754 (GRCm39) |
I23F |
probably benign |
Het |
| Muc21 |
G |
A |
17: 35,929,761 (GRCm39) |
A1475V |
unknown |
Het |
| Myocos |
T |
C |
1: 162,484,687 (GRCm39) |
R41G |
unknown |
Het |
| Myod1 |
A |
G |
7: 46,027,643 (GRCm39) |
D261G |
probably benign |
Het |
| Nop14 |
C |
T |
5: 34,796,376 (GRCm39) |
R781Q |
probably damaging |
Het |
| Nsmaf |
A |
G |
4: 6,438,083 (GRCm39) |
V63A |
probably benign |
Het |
| Ntsr1 |
A |
T |
2: 180,142,725 (GRCm39) |
H172L |
probably damaging |
Het |
| Or4k6 |
T |
C |
14: 50,476,073 (GRCm39) |
K90E |
probably damaging |
Het |
| Or8b1c |
A |
T |
9: 38,384,739 (GRCm39) |
E232V |
probably benign |
Het |
| Pcdha11 |
T |
C |
18: 37,139,979 (GRCm39) |
V536A |
probably damaging |
Het |
| Prps1l1 |
T |
A |
12: 35,035,679 (GRCm39) |
C265S |
probably benign |
Het |
| Prune2 |
A |
G |
19: 17,097,261 (GRCm39) |
S922G |
probably benign |
Het |
| Qpctl |
A |
T |
7: 18,883,055 (GRCm39) |
M19K |
probably benign |
Het |
| Rad51 |
C |
T |
2: 118,964,599 (GRCm39) |
T230I |
possibly damaging |
Het |
| Rad9b |
A |
G |
5: 122,472,341 (GRCm39) |
F246L |
possibly damaging |
Het |
| Rarb |
A |
T |
14: 16,508,932 (GRCm38) |
|
probably null |
Het |
| Sdcbp2 |
T |
C |
2: 151,429,321 (GRCm39) |
S214P |
possibly damaging |
Het |
| Slc22a1 |
T |
A |
17: 12,875,892 (GRCm39) |
M441L |
probably benign |
Het |
| Slc35f1 |
G |
A |
10: 52,938,637 (GRCm39) |
V190I |
probably benign |
Het |
| Spon1 |
A |
T |
7: 113,629,475 (GRCm39) |
Q373L |
possibly damaging |
Het |
| Ssbp2 |
T |
A |
13: 91,842,122 (GRCm39) |
|
probably null |
Het |
| Sult1e1 |
T |
A |
5: 87,726,512 (GRCm39) |
R201* |
probably null |
Het |
| Traj32 |
T |
A |
14: 54,423,606 (GRCm39) |
L16Q |
|
Het |
| Ttc16 |
T |
C |
2: 32,664,437 (GRCm39) |
I67V |
probably null |
Het |
| Ttn |
T |
A |
2: 76,556,899 (GRCm39) |
K30035N |
probably damaging |
Het |
| Ttn |
T |
A |
2: 76,776,473 (GRCm39) |
Y1607F |
unknown |
Het |
| Usp16 |
G |
A |
16: 87,268,977 (GRCm39) |
R290H |
probably benign |
Het |
| Utp3 |
G |
C |
5: 88,702,376 (GRCm39) |
|
probably benign |
Het |
| Xpnpep3 |
A |
G |
15: 81,298,735 (GRCm39) |
H56R |
probably damaging |
Het |
| Zfp592 |
G |
T |
7: 80,674,070 (GRCm39) |
D345Y |
probably damaging |
Het |
| Zfp931 |
A |
T |
2: 177,709,824 (GRCm39) |
Y187* |
probably null |
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 |
|
R5090:Pcdha6
|
UTSW |
18 |
37,101,770 (GRCm39) |
missense |
probably benign |
0.15 |
|
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 |
|
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'- ATTACTCCGTCCCAGAGGAG -3'
(R):5'- GTTTGATTTCACATCTAGCCCAAAG -3'
Sequencing Primer
(F):5'- TTCAGGGTGGCGTCCAAG -3'
(R):5'- TAGCCCAAAGTATTCGCTGG -3'
|
| Posted On |
2019-06-26 |
Incidental Mutation