Incidental Mutation 'R3875:Pcdha6'
| ID |
474327 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha6
|
| Ensembl Gene |
ENSMUSG00000103707 |
| Gene Name |
protocadherin alpha 6 |
| Synonyms |
Cnr2, Crnr2 |
| MMRRC Submission |
068967-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.172)
|
| Stock # |
R3875 (G1)
|
| Quality Score |
211 |
|
Status
|
Not validated
|
| Chromosome |
18 |
| Chromosomal Location |
37100684-37320710 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 37101119 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Asparagine
at position 104
(I104N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000142285
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000070797]
[ENSMUST00000115661]
[ENSMUST00000115662]
[ENSMUST00000192168]
[ENSMUST00000192295]
[ENSMUST00000192503]
[ENSMUST00000194751]
[ENSMUST00000193389]
[ENSMUST00000193777]
[ENSMUST00000192512]
[ENSMUST00000194544]
[ENSMUST00000195590]
[ENSMUST00000193839]
|
| 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 damaging
Transcript: ENSMUST00000194751
AA Change: I104N
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000142285
Gene: ENSMUSG00000103707
AA Change: I104N
| 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 damaging
Transcript: ENSMUST00000193389
AA Change: I104N
PolyPhen 2
Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000141459
Gene: ENSMUSG00000103707
AA Change: I104N
| 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: I104N
PolyPhen 2
Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000141587
Gene: ENSMUSG00000103707
AA Change: I104N
| 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: 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: 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: 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 |
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.6%
- 20x: 96.1%
|
| Validation Efficiency |
100% (50/50) |
| 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: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 6820408C15Rik |
T |
C |
2: 152,276,000 (GRCm39) |
S72P |
probably benign |
Het |
| Abca5 |
T |
A |
11: 110,201,059 (GRCm39) |
Y447F |
probably damaging |
Het |
| Adgrg2 |
A |
G |
X: 159,261,992 (GRCm39) |
S337G |
probably benign |
Het |
| Akap12 |
G |
A |
10: 4,307,590 (GRCm39) |
V1467I |
probably benign |
Het |
| Baz2a |
T |
A |
10: 127,959,979 (GRCm39) |
M1419K |
probably damaging |
Het |
| Cacna1g |
G |
A |
11: 94,328,749 (GRCm39) |
T1033I |
probably damaging |
Het |
| Car12 |
C |
A |
9: 66,624,834 (GRCm39) |
|
probably benign |
Het |
| Cpne1 |
G |
A |
2: 155,918,202 (GRCm39) |
H352Y |
probably damaging |
Het |
| D630039A03Rik |
T |
A |
4: 57,910,606 (GRCm39) |
T69S |
probably benign |
Het |
| Dhodh |
T |
C |
8: 110,321,592 (GRCm39) |
D310G |
probably null |
Het |
| Dnah2 |
A |
G |
11: 69,320,174 (GRCm39) |
I3965T |
probably damaging |
Het |
| Drd5 |
T |
G |
5: 38,477,157 (GRCm39) |
V50G |
possibly damaging |
Het |
| Dst |
C |
A |
1: 34,210,328 (GRCm39) |
H934Q |
probably damaging |
Het |
| Eif1ad10 |
T |
C |
12: 88,216,476 (GRCm39) |
D132G |
unknown |
Het |
| Far2 |
G |
A |
6: 148,052,089 (GRCm39) |
E123K |
probably benign |
Het |
| Fbxo43 |
A |
T |
15: 36,162,249 (GRCm39) |
F319L |
probably benign |
Het |
| Flii |
T |
C |
11: 60,611,318 (GRCm39) |
S418G |
probably benign |
Het |
| Glyctk |
T |
A |
9: 106,034,820 (GRCm39) |
Y82F |
probably damaging |
Het |
| Gm11353 |
G |
T |
13: 26,676,651 (GRCm39) |
|
noncoding transcript |
Het |
| Gm6505 |
T |
A |
3: 28,819,286 (GRCm39) |
|
noncoding transcript |
Het |
| Gpr151 |
A |
G |
18: 42,711,661 (GRCm39) |
V339A |
probably benign |
Het |
| H2-T22 |
T |
C |
17: 36,351,195 (GRCm39) |
I296V |
probably benign |
Het |
| Igfn1 |
T |
C |
1: 135,882,352 (GRCm39) |
N2831S |
probably damaging |
Het |
| Igkv13-85 |
A |
G |
6: 68,907,484 (GRCm39) |
V39A |
probably damaging |
Het |
| Irx5 |
A |
G |
8: 93,086,793 (GRCm39) |
T242A |
probably benign |
Het |
| Krt26 |
T |
C |
11: 99,225,570 (GRCm39) |
K304E |
probably damaging |
Het |
| Mcoln1 |
A |
G |
8: 3,558,355 (GRCm39) |
D203G |
probably benign |
Het |
| Mlph |
T |
C |
1: 90,855,844 (GRCm39) |
C57R |
probably damaging |
Het |
| Myh13 |
C |
A |
11: 67,249,020 (GRCm39) |
H1275Q |
probably benign |
Het |
| Nbeal1 |
T |
A |
1: 60,233,758 (GRCm39) |
|
probably benign |
Het |
| Orc5 |
T |
A |
5: 22,742,564 (GRCm39) |
M115L |
probably benign |
Het |
| Plcb4 |
T |
C |
2: 135,844,552 (GRCm39) |
S157P |
probably damaging |
Het |
| Polq |
A |
G |
16: 36,894,389 (GRCm39) |
D1787G |
probably damaging |
Het |
| Prkar2b |
T |
G |
12: 32,015,122 (GRCm39) |
I142L |
probably benign |
Het |
| Ptprq |
A |
G |
10: 107,520,965 (GRCm39) |
S736P |
possibly damaging |
Het |
| Qrich2 |
A |
T |
11: 116,336,477 (GRCm39) |
V2046D |
probably damaging |
Het |
| Rad21 |
A |
T |
15: 51,833,361 (GRCm39) |
F373I |
probably damaging |
Het |
| Rcvrn |
A |
G |
11: 67,590,880 (GRCm39) |
I155V |
probably benign |
Het |
| Rsrc2 |
C |
T |
5: 123,874,691 (GRCm39) |
|
probably benign |
Het |
| Sgsh |
A |
G |
11: 119,241,773 (GRCm39) |
L111P |
probably damaging |
Het |
| Ssc5d |
A |
T |
7: 4,930,261 (GRCm39) |
D114V |
probably damaging |
Het |
| St6gal2 |
C |
A |
17: 55,789,698 (GRCm39) |
P244Q |
probably benign |
Het |
| Tarbp1 |
A |
G |
8: 127,165,538 (GRCm39) |
|
probably benign |
Het |
| Tmem221 |
T |
C |
8: 72,008,399 (GRCm39) |
|
probably null |
Het |
| Trh |
A |
T |
6: 92,220,679 (GRCm39) |
V61E |
possibly damaging |
Het |
| Trim32 |
A |
T |
4: 65,531,703 (GRCm39) |
I87F |
possibly damaging |
Het |
| Tti2 |
A |
G |
8: 31,641,175 (GRCm39) |
K100E |
probably benign |
Het |
| Usp34 |
C |
T |
11: 23,439,033 (GRCm39) |
P3532S |
possibly damaging |
Het |
| Vps13d |
A |
G |
4: 144,917,114 (GRCm39) |
Y17H |
probably damaging |
Het |
| Zfp106 |
T |
C |
2: 120,365,094 (GRCm39) |
K438E |
probably benign |
Het |
| Zfp60 |
T |
C |
7: 27,449,006 (GRCm39) |
I558T |
probably damaging |
Het |
| Zzef1 |
A |
C |
11: 72,779,866 (GRCm39) |
I1880L |
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 |
|
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 |
|
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 |
|
| Posted On |
2017-04-14 |
Incidental Mutation