Incidental Mutation 'R5084:Pcdha6'
ID |
387343 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Pcdha6
|
Ensembl Gene |
ENSMUSG00000103707 |
Gene Name |
protocadherin alpha 6 |
Synonyms |
Cnr2, Crnr2 |
MMRRC Submission |
042673-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.156)
|
Stock # |
R5084 (G1)
|
Quality Score |
225 |
Status
|
Not validated
|
Chromosome |
18 |
Chromosomal Location |
37100684-37320710 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 37102016 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Asparagine to Isoleucine
at position 403
(N403I)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000141587
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000070797]
[ENSMUST00000115661]
[ENSMUST00000115662]
[ENSMUST00000192168]
[ENSMUST00000192295]
[ENSMUST00000192503]
[ENSMUST00000193389]
[ENSMUST00000193777]
[ENSMUST00000192512]
[ENSMUST00000195590]
[ENSMUST00000193839]
[ENSMUST00000194751]
[ENSMUST00000192631]
[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 damaging
Transcript: ENSMUST00000193389
AA Change: N403I
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000141459 Gene: ENSMUSG00000103707 AA Change: N403I
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: N403I
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000141587 Gene: ENSMUSG00000103707 AA Change: N403I
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: 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: 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: 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 benign
Transcript: ENSMUST00000194544
|
SMART Domains |
Protein: ENSMUSP00000141847 Gene: ENSMUSG00000102836
Domain | Start | End | E-Value | Type |
Blast:CA
|
18 |
66 |
5e-20 |
BLAST |
|
Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.4%
- 10x: 96.3%
- 20x: 92.4%
|
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: 57 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Acp3 |
T |
A |
9: 104,204,116 (GRCm39) |
E59D |
probably damaging |
Het |
Akap7 |
T |
A |
10: 25,155,640 (GRCm39) |
|
probably benign |
Het |
Anpep |
C |
A |
7: 79,476,618 (GRCm39) |
|
probably null |
Het |
Aste1 |
T |
A |
9: 105,274,886 (GRCm39) |
Y314* |
probably null |
Het |
Ccdc183 |
G |
A |
2: 25,498,802 (GRCm39) |
T497I |
probably damaging |
Het |
Cd4 |
A |
T |
6: 124,847,402 (GRCm39) |
I254N |
probably damaging |
Het |
Crot |
G |
T |
5: 9,019,994 (GRCm39) |
H449Q |
probably damaging |
Het |
Dact2 |
A |
T |
17: 14,418,214 (GRCm39) |
W164R |
possibly damaging |
Het |
Dapk3 |
C |
A |
10: 81,026,152 (GRCm39) |
|
probably null |
Het |
Dnase1l1 |
C |
T |
X: 73,320,644 (GRCm39) |
|
probably null |
Het |
Fbrsl1 |
G |
A |
5: 110,527,272 (GRCm39) |
|
probably benign |
Het |
Flg |
T |
C |
3: 93,184,922 (GRCm39) |
F15L |
probably damaging |
Het |
Fscn2 |
A |
G |
11: 120,252,686 (GRCm39) |
D51G |
probably damaging |
Het |
H2-Ob |
G |
T |
17: 34,460,102 (GRCm39) |
G71V |
probably damaging |
Het |
Hmgcs1 |
T |
C |
13: 120,161,520 (GRCm39) |
V104A |
possibly damaging |
Het |
Hs3st4 |
G |
T |
7: 123,996,518 (GRCm39) |
D395Y |
probably damaging |
Het |
Itgb4 |
C |
T |
11: 115,874,983 (GRCm39) |
R447W |
probably benign |
Het |
Ldlrad3 |
G |
A |
2: 101,900,329 (GRCm39) |
R58C |
probably damaging |
Het |
Lpin1 |
A |
G |
12: 16,626,983 (GRCm39) |
S188P |
probably damaging |
Het |
Mamdc2 |
G |
T |
19: 23,336,516 (GRCm39) |
T331K |
possibly damaging |
Het |
Matr3 |
G |
A |
18: 35,715,135 (GRCm39) |
S195N |
probably damaging |
Het |
Nktr |
T |
C |
9: 121,577,176 (GRCm39) |
Y390H |
possibly damaging |
Het |
Notch3 |
C |
T |
17: 32,376,864 (GRCm39) |
|
probably null |
Het |
Olfm3 |
T |
C |
3: 114,698,202 (GRCm39) |
|
probably null |
Het |
Or10ak11 |
A |
G |
4: 118,686,767 (GRCm39) |
V290A |
probably damaging |
Het |
Or2a20 |
T |
C |
6: 43,194,594 (GRCm39) |
L249P |
probably damaging |
Het |
Or5h25 |
C |
T |
16: 58,930,436 (GRCm39) |
C179Y |
possibly damaging |
Het |
Or7e173 |
T |
A |
9: 19,938,551 (GRCm39) |
I228F |
probably damaging |
Het |
Or7g17 |
T |
A |
9: 18,768,632 (GRCm39) |
M237K |
probably benign |
Het |
Pask |
A |
G |
1: 93,249,819 (GRCm39) |
V527A |
probably benign |
Het |
Peg3 |
T |
C |
7: 6,710,848 (GRCm39) |
E1458G |
probably damaging |
Het |
Pip4k2b |
G |
A |
11: 97,610,569 (GRCm39) |
T386M |
probably damaging |
Het |
Pkd1l1 |
T |
C |
11: 8,892,004 (GRCm39) |
M272V |
probably benign |
Het |
Plcb4 |
A |
G |
2: 135,844,571 (GRCm39) |
E163G |
probably damaging |
Het |
Plk5 |
C |
A |
10: 80,194,723 (GRCm39) |
R149S |
possibly damaging |
Het |
Pou4f3 |
A |
T |
18: 42,528,933 (GRCm39) |
Y292F |
probably damaging |
Het |
Rasgef1c |
A |
G |
11: 49,860,332 (GRCm39) |
K272E |
probably damaging |
Het |
Rbl2 |
C |
T |
8: 91,841,759 (GRCm39) |
T942M |
probably benign |
Het |
Sipa1l3 |
G |
A |
7: 29,048,000 (GRCm39) |
S247F |
probably damaging |
Het |
Smarca4 |
T |
C |
9: 21,572,059 (GRCm39) |
L777P |
probably damaging |
Het |
Smpd1 |
T |
C |
7: 105,206,185 (GRCm39) |
Y438H |
probably damaging |
Het |
Sorl1 |
T |
C |
9: 41,887,673 (GRCm39) |
K2052R |
probably benign |
Het |
Spata31d1c |
C |
A |
13: 65,182,944 (GRCm39) |
P162Q |
probably damaging |
Het |
Spmip9 |
A |
G |
6: 70,892,688 (GRCm39) |
S20P |
possibly damaging |
Het |
Ston1 |
A |
T |
17: 88,944,002 (GRCm39) |
E469D |
probably benign |
Het |
Syde2 |
AGTTC |
AGTTCGTTC |
3: 145,707,164 (GRCm39) |
|
probably null |
Het |
Syde2 |
CAGTT |
CAGTTAGTT |
3: 145,707,163 (GRCm39) |
|
probably null |
Het |
Taar5 |
T |
A |
10: 23,846,836 (GRCm39) |
L78Q |
probably damaging |
Het |
Tas2r114 |
A |
T |
6: 131,666,251 (GRCm39) |
L259* |
probably null |
Het |
Topaz1 |
T |
A |
9: 122,577,883 (GRCm39) |
H264Q |
probably benign |
Het |
Vcl |
G |
T |
14: 21,059,027 (GRCm39) |
V548L |
possibly damaging |
Het |
Vmn2r57 |
C |
A |
7: 41,075,974 (GRCm39) |
|
probably null |
Het |
Vmn2r92 |
A |
G |
17: 18,405,439 (GRCm39) |
*861W |
probably null |
Het |
Ylpm1 |
T |
G |
12: 85,076,095 (GRCm39) |
V940G |
probably damaging |
Het |
Zfp236 |
A |
G |
18: 82,627,556 (GRCm39) |
S1500P |
probably damaging |
Het |
Zfp384 |
G |
T |
6: 125,000,642 (GRCm39) |
|
probably benign |
Het |
Zfp786 |
T |
C |
6: 47,796,953 (GRCm39) |
M662V |
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 |
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 |
PCR Primer
(F):5'- ATGTGCCTCAGATCACTTTGAC -3'
(R):5'- CGCCGATACTGTGAAGATGTG -3'
Sequencing Primer
(F):5'- AGATCACTTTGACTTCCTTATCCCTG -3'
(R):5'- ATACTGTGAAGATGTGCGCTCCAG -3'
|
Posted On |
2016-06-06 |