Incidental Mutation 'R8513:Pcdha6'
| ID |
656002 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha6
|
| Ensembl Gene |
ENSMUSG00000103707 |
| Gene Name |
protocadherin alpha 6 |
| Synonyms |
Cnr2, Crnr2 |
| MMRRC Submission |
067889-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.172)
|
| Stock # |
R8513 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
18 |
| Chromosomal Location |
37100684-37320710 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 37102229 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Threonine
at position 474
(I474T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000141587
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000070797]
[ENSMUST00000115661]
[ENSMUST00000115662]
[ENSMUST00000192168]
[ENSMUST00000192295]
[ENSMUST00000192503]
[ENSMUST00000192512]
[ENSMUST00000193777]
[ENSMUST00000192631]
[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: I474T
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000141587
Gene: ENSMUSG00000103707
AA Change: I474T
| 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: 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 damaging
Transcript: ENSMUST00000193389
AA Change: I474T
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000141459
Gene: ENSMUSG00000103707
AA Change: I474T
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.5%
- 20x: 98.5%
|
| 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: 41 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Apoe |
C |
A |
7: 19,430,565 (GRCm39) |
G226W |
probably damaging |
Het |
| Armc9 |
T |
C |
1: 86,090,405 (GRCm39) |
F67L |
probably damaging |
Het |
| Bsn |
T |
C |
9: 107,991,709 (GRCm39) |
I1348V |
possibly damaging |
Het |
| Cdc73 |
C |
A |
1: 143,493,129 (GRCm39) |
E402* |
probably null |
Het |
| Coro2a |
ACCAGAAGAGCCATCCAG |
ACCAG |
4: 46,544,117 (GRCm39) |
|
probably null |
Het |
| Cpt2 |
G |
A |
4: 107,764,123 (GRCm39) |
A547V |
probably damaging |
Het |
| Cpxm2 |
A |
T |
7: 131,745,431 (GRCm39) |
H131Q |
probably benign |
Het |
| Ctdp1 |
G |
A |
18: 80,492,678 (GRCm39) |
L606F |
possibly damaging |
Het |
| Dot1l |
T |
C |
10: 80,627,260 (GRCm39) |
S1494P |
possibly damaging |
Het |
| Evpl |
C |
T |
11: 116,120,570 (GRCm39) |
|
probably null |
Het |
| Fgd3 |
T |
C |
13: 49,417,400 (GRCm39) |
T688A |
probably benign |
Het |
| Galnt3 |
A |
T |
2: 65,924,064 (GRCm39) |
C401* |
probably null |
Het |
| Gml2 |
C |
G |
15: 74,696,004 (GRCm39) |
P133A |
probably damaging |
Het |
| Hepacam |
A |
G |
9: 37,291,930 (GRCm39) |
E86G |
probably benign |
Het |
| Ilf3 |
A |
G |
9: 21,299,932 (GRCm39) |
E39G |
possibly damaging |
Het |
| Kdm3b |
G |
T |
18: 34,926,129 (GRCm39) |
A90S |
probably benign |
Het |
| Kiz |
A |
G |
2: 146,712,684 (GRCm39) |
|
probably null |
Het |
| Myo1e |
T |
A |
9: 70,227,370 (GRCm39) |
L147H |
probably damaging |
Het |
| Naa15 |
T |
A |
3: 51,367,444 (GRCm39) |
V539E |
probably damaging |
Het |
| Nlrp6 |
A |
C |
7: 140,502,743 (GRCm39) |
D283A |
possibly damaging |
Het |
| Ntf5 |
A |
G |
7: 45,065,179 (GRCm39) |
T104A |
probably damaging |
Het |
| Or1e28-ps1 |
A |
G |
11: 73,615,148 (GRCm39) |
V234A |
unknown |
Het |
| Pacsin3 |
A |
C |
2: 91,093,150 (GRCm39) |
N214T |
probably benign |
Het |
| Pcdhgb1 |
A |
G |
18: 37,813,581 (GRCm39) |
Y24C |
probably damaging |
Het |
| Pde2a |
A |
T |
7: 101,158,972 (GRCm39) |
N749Y |
probably damaging |
Het |
| Ptpn3 |
G |
A |
4: 57,270,085 (GRCm39) |
R26* |
probably null |
Het |
| Rab7 |
T |
C |
6: 87,981,250 (GRCm39) |
Y144C |
probably benign |
Het |
| Ralgps1 |
T |
C |
2: 33,226,626 (GRCm39) |
S22G |
probably damaging |
Het |
| Setdb2 |
G |
A |
14: 59,639,839 (GRCm39) |
T668M |
probably damaging |
Het |
| Slit2 |
T |
A |
5: 48,382,050 (GRCm39) |
C510* |
probably null |
Het |
| Snrpa1 |
G |
A |
7: 65,720,381 (GRCm39) |
G195R |
probably benign |
Het |
| Spata2l |
T |
C |
8: 123,960,438 (GRCm39) |
M284V |
probably benign |
Het |
| Spata31d1c |
G |
T |
13: 65,180,991 (GRCm39) |
S30I |
probably damaging |
Het |
| Stab1 |
C |
A |
14: 30,871,747 (GRCm39) |
|
probably null |
Het |
| Tmem184b |
A |
T |
15: 79,254,123 (GRCm39) |
S142T |
probably benign |
Het |
| Tmem201 |
A |
T |
4: 149,812,380 (GRCm39) |
M312K |
probably damaging |
Het |
| Tpp1 |
A |
T |
7: 105,398,786 (GRCm39) |
D214E |
possibly damaging |
Het |
| Trav7-2 |
C |
T |
14: 53,628,478 (GRCm39) |
S72F |
probably damaging |
Het |
| Vmn1r37 |
A |
G |
6: 66,708,820 (GRCm39) |
T149A |
probably benign |
Het |
| Zfp512 |
T |
C |
5: 31,637,425 (GRCm39) |
S505P |
probably damaging |
Het |
| Zfp942 |
T |
C |
17: 22,147,282 (GRCm39) |
D449G |
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 |
|
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 |
|
|
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'- GACCACAGCTGACTATCAGG -3'
(R):5'- AGAGTCACATTGCTGCCCAG -3'
Sequencing Primer
(F):5'- ACTATCAGGTGGTGGTGACAG -3'
(R):5'- TCACCTGGAACTGCAGCAG -3'
|
| Posted On |
2020-10-20 |
Incidental Mutation