Incidental Mutation 'R6889:Pcdha6'
| ID |
537140 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha6
|
| Ensembl Gene |
ENSMUSG00000103707 |
| Gene Name |
protocadherin alpha 6 |
| Synonyms |
Crnr2, Cnr2 |
| MMRRC Submission |
044983-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.141)
|
| Stock # |
R6889 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
18 |
| Chromosomal Location |
36967631-37187657 bp(+) (GRCm38) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to T
at 36968343 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Phenylalanine
at position 196
(L196F)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000141587
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000070797]
[ENSMUST00000115661]
[ENSMUST00000115662]
[ENSMUST00000192168]
[ENSMUST00000192295]
[ENSMUST00000192503]
[ENSMUST00000192512]
[ENSMUST00000193389]
[ENSMUST00000193777]
[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: ENSMUST00000193389
AA Change: L196F
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000141459
Gene: ENSMUSG00000103707
AA Change: L196F
| 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: L196F
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000141587
Gene: ENSMUSG00000103707
AA Change: L196F
| 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: 99.9%
- 10x: 99.4%
- 20x: 98.1%
|
| Validation Efficiency |
|
| 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 |
|---|
| 2310002L09Rik |
A |
T |
4: 73,943,053 (GRCm38) |
D103E |
probably benign |
Het |
| Abcc3 |
A |
T |
11: 94,375,555 (GRCm38) |
S70T |
possibly damaging |
Het |
| Atp6v0a1 |
A |
G |
11: 101,029,183 (GRCm38) |
Y214C |
possibly damaging |
Het |
| Azi2 |
A |
G |
9: 118,049,895 (GRCm38) |
|
probably null |
Het |
| BC067074 |
C |
A |
13: 113,318,378 (GRCm38) |
S319R |
probably damaging |
Het |
| Cacnb2 |
T |
A |
2: 14,986,015 (GRCm38) |
V636E |
possibly damaging |
Het |
| Cd8a |
A |
C |
6: 71,374,562 (GRCm38) |
T169P |
probably damaging |
Het |
| Cfap44 |
G |
A |
16: 44,404,132 (GRCm38) |
V68I |
probably benign |
Het |
| Eea1 |
G |
T |
10: 96,037,478 (GRCm38) |
C1134F |
probably benign |
Het |
| Ehmt2 |
T |
G |
17: 34,912,772 (GRCm38) |
F1192V |
probably damaging |
Het |
| Emc1 |
T |
C |
4: 139,365,350 (GRCm38) |
F531L |
probably damaging |
Het |
| Eme1 |
G |
A |
11: 94,650,477 (GRCm38) |
T173I |
probably benign |
Het |
| Gli2 |
A |
T |
1: 118,844,416 (GRCm38) |
C520S |
probably damaging |
Het |
| Gm43302 |
T |
C |
5: 105,280,138 (GRCm38) |
K186E |
probably benign |
Het |
| Gpr108 |
A |
T |
17: 57,236,990 (GRCm38) |
N405K |
probably damaging |
Het |
| Hmgcl |
C |
A |
4: 135,955,642 (GRCm38) |
T135N |
probably benign |
Het |
| Hydin |
G |
A |
8: 110,532,856 (GRCm38) |
D2487N |
possibly damaging |
Het |
| Igfl3 |
G |
T |
7: 18,179,800 (GRCm38) |
R25L |
probably benign |
Het |
| Igsf10 |
A |
C |
3: 59,331,933 (GRCm38) |
S276A |
probably benign |
Het |
| Kctd1 |
A |
G |
18: 14,973,988 (GRCm38) |
S211P |
probably damaging |
Het |
| Kctd7 |
A |
T |
5: 130,152,501 (GRCm38) |
Q255L |
probably benign |
Het |
| Lrig1 |
A |
G |
6: 94,625,063 (GRCm38) |
Y270H |
probably benign |
Het |
| Muc5ac |
C |
T |
7: 141,809,744 (GRCm38) |
|
probably benign |
Het |
| Myh15 |
A |
G |
16: 49,153,111 (GRCm38) |
N1248S |
possibly damaging |
Het |
| Nod1 |
A |
G |
6: 54,944,109 (GRCm38) |
F408S |
probably benign |
Het |
| Nrp1 |
T |
C |
8: 128,493,057 (GRCm38) |
F652S |
probably damaging |
Het |
| Olfr1338 |
G |
A |
4: 118,754,307 (GRCm38) |
T79I |
probably damaging |
Het |
| Olfr487 |
A |
T |
7: 108,211,918 (GRCm38) |
F204I |
probably benign |
Het |
| Olfr574 |
A |
T |
7: 102,948,768 (GRCm38) |
H91L |
possibly damaging |
Het |
| Olfr821 |
T |
C |
10: 130,034,532 (GRCm38) |
M302T |
probably benign |
Het |
| Opa1 |
G |
T |
16: 29,620,868 (GRCm38) |
R792L |
probably benign |
Het |
| Pdia2 |
A |
T |
17: 26,196,970 (GRCm38) |
Y347* |
probably null |
Het |
| Pdpr |
G |
T |
8: 111,124,613 (GRCm38) |
|
probably null |
Het |
| Pigt |
T |
A |
2: 164,507,331 (GRCm38) |
L518Q |
probably damaging |
Het |
| Ppfibp2 |
A |
C |
7: 107,737,981 (GRCm38) |
D591A |
possibly damaging |
Het |
| Prrg2 |
G |
A |
7: 45,059,989 (GRCm38) |
T97M |
possibly damaging |
Het |
| Qars |
A |
G |
9: 108,513,183 (GRCm38) |
T428A |
probably damaging |
Het |
| Rai1 |
T |
C |
11: 60,185,715 (GRCm38) |
F202L |
probably damaging |
Het |
| Rars |
A |
T |
11: 35,808,486 (GRCm38) |
M660K |
probably damaging |
Het |
| Rsf1 |
GCGGCGGCG |
GCGGCGGCGTCGGCGGCG |
7: 97,579,925 (GRCm38) |
|
probably benign |
Het |
| Slc16a6 |
A |
C |
11: 109,455,040 (GRCm38) |
F382V |
probably damaging |
Het |
| Slc30a7 |
T |
C |
3: 115,954,153 (GRCm38) |
T330A |
probably damaging |
Het |
| Smc1b |
A |
T |
15: 85,067,759 (GRCm38) |
L1157Q |
probably damaging |
Het |
| Snx4 |
G |
T |
16: 33,251,470 (GRCm38) |
A4S |
possibly damaging |
Het |
| Sv2b |
A |
C |
7: 75,125,767 (GRCm38) |
|
probably null |
Het |
| Syt9 |
A |
T |
7: 107,425,286 (GRCm38) |
I129L |
probably damaging |
Het |
| Ttbk2 |
T |
C |
2: 120,773,353 (GRCm38) |
E198G |
probably damaging |
Het |
| Ubr3 |
A |
T |
2: 69,944,300 (GRCm38) |
D488V |
possibly damaging |
Het |
| Ush2a |
T |
A |
1: 188,797,871 (GRCm38) |
C3286S |
probably damaging |
Het |
| Vill |
A |
G |
9: 119,065,882 (GRCm38) |
D56G |
possibly damaging |
Het |
| Vmn1r41 |
A |
T |
6: 89,747,370 (GRCm38) |
I298F |
probably damaging |
Het |
| Vmn2r2 |
A |
T |
3: 64,117,267 (GRCm38) |
V631D |
probably damaging |
Het |
| Vmn2r32 |
A |
G |
7: 7,472,574 (GRCm38) |
S437P |
possibly damaging |
Het |
| Vmn2r53 |
A |
G |
7: 12,601,142 (GRCm38) |
V197A |
probably benign |
Het |
| Wasf1 |
A |
T |
10: 40,920,369 (GRCm38) |
I32F |
probably damaging |
Het |
| Wasf2 |
G |
T |
4: 133,194,730 (GRCm38) |
A387S |
unknown |
Het |
| Wdr92 |
G |
A |
11: 17,222,309 (GRCm38) |
V133M |
probably damaging |
Het |
| Zbtb14 |
G |
A |
17: 69,387,679 (GRCm38) |
C124Y |
probably damaging |
Het |
| Zfp462 |
G |
T |
4: 55,007,671 (GRCm38) |
A37S |
probably damaging |
Het |
| Zfp532 |
A |
G |
18: 65,686,990 (GRCm38) |
E882G |
possibly damaging |
Het |
|
| Other mutations in Pcdha6 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
R3734:Pcdha6
|
UTSW |
18 |
36,969,401 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R3859:Pcdha6
|
UTSW |
18 |
36,969,931 (GRCm38) |
missense |
possibly damaging |
0.89 |
|
R3875:Pcdha6
|
UTSW |
18 |
36,968,066 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4446:Pcdha6
|
UTSW |
18 |
36,967,760 (GRCm38) |
missense |
probably benign |
0.28 |
|
R4647:Pcdha6
|
UTSW |
18 |
36,969,136 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R4659:Pcdha6
|
UTSW |
18 |
36,969,239 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4780:Pcdha6
|
UTSW |
18 |
36,969,853 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R4839:Pcdha6
|
UTSW |
18 |
36,968,432 (GRCm38) |
missense |
possibly damaging |
0.73 |
|
R4915:Pcdha6
|
UTSW |
18 |
36,968,457 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5011:Pcdha6
|
UTSW |
18 |
36,967,907 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5084:Pcdha6
|
UTSW |
18 |
36,968,963 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5090:Pcdha6
|
UTSW |
18 |
36,968,717 (GRCm38) |
missense |
probably benign |
0.15 |
|
R5189:Pcdha6
|
UTSW |
18 |
36,968,791 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R5652:Pcdha6
|
UTSW |
18 |
36,968,836 (GRCm38) |
splice site |
probably null |
|
|
R5773:Pcdha6
|
UTSW |
18 |
36,969,590 (GRCm38) |
missense |
probably benign |
0.00 |
|
R5890:Pcdha6
|
UTSW |
18 |
36,969,068 (GRCm38) |
missense |
possibly damaging |
0.94 |
|
R6135:Pcdha6
|
UTSW |
18 |
36,969,216 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R6276:Pcdha6
|
UTSW |
18 |
36,969,767 (GRCm38) |
splice site |
probably null |
|
|
R6346:Pcdha6
|
UTSW |
18 |
36,968,060 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R7295:Pcdha6
|
UTSW |
18 |
36,968,136 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R7776:Pcdha6
|
UTSW |
18 |
36,969,981 (GRCm38) |
missense |
probably benign |
0.27 |
|
R7944:Pcdha6
|
UTSW |
18 |
36,968,912 (GRCm38) |
missense |
possibly damaging |
0.55 |
|
R7950:Pcdha6
|
UTSW |
18 |
36,969,426 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R8371:Pcdha6
|
UTSW |
18 |
36,969,867 (GRCm38) |
nonsense |
probably null |
|
|
R8513:Pcdha6
|
UTSW |
18 |
36,969,176 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R8549:Pcdha6
|
UTSW |
18 |
36,968,541 (GRCm38) |
missense |
possibly damaging |
0.83 |
|
R8735:Pcdha6
|
UTSW |
18 |
36,968,150 (GRCm38) |
missense |
possibly damaging |
0.55 |
|
R8827:Pcdha6
|
UTSW |
18 |
36,969,749 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R8881:Pcdha6
|
UTSW |
18 |
36,968,431 (GRCm38) |
missense |
probably damaging |
1.00 |
|
R9094:Pcdha6
|
UTSW |
18 |
36,968,540 (GRCm38) |
missense |
probably damaging |
0.98 |
|
R9357:Pcdha6
|
UTSW |
18 |
36,969,173 (GRCm38) |
missense |
probably benign |
0.16 |
|
Z1088:Pcdha6
|
UTSW |
18 |
36,969,217 (GRCm38) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGATAACCCGCCTGTGTTC -3'
(R):5'- AACTGTCGTTCCGTTGTCTG -3'
Sequencing Primer
(F):5'- ATAACCCGCCTGTGTTCTCAGTAAAG -3'
(R):5'- CCGTTGTCTGAGTTTTCCAAG -3'
|
| Posted On |
2018-10-18 |
Incidental Mutation