Incidental Mutation 'R4446:Pcdha6'
| ID |
329915 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha6
|
| Ensembl Gene |
ENSMUSG00000103707 |
| Gene Name |
protocadherin alpha 6 |
| Synonyms |
Cnr2, Crnr2 |
| MMRRC Submission |
041707-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.172)
|
| Stock # |
R4446 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
37100684-37320710 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 37100813 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 2
(D2G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000142285
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000070797]
[ENSMUST00000115661]
[ENSMUST00000115662]
[ENSMUST00000192168]
[ENSMUST00000192295]
[ENSMUST00000192503]
[ENSMUST00000194751]
[ENSMUST00000193389]
[ENSMUST00000193777]
[ENSMUST00000192512]
[ENSMUST00000195590]
[ENSMUST00000193839]
[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 benign
Transcript: ENSMUST00000194751
AA Change: D2G
PolyPhen 2
Score 0.285 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000142285
Gene: ENSMUSG00000103707
AA Change: D2G
| 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: ENSMUST00000193389
AA Change: D2G
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000141459
Gene: ENSMUSG00000103707
AA Change: D2G
| 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: ENSMUST00000193777
AA Change: D2G
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000141587
Gene: ENSMUSG00000103707
AA Change: D2G
| 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: ENSMUST00000194544
|
| SMART Domains |
Protein: ENSMUSP00000141847
Gene: ENSMUSG00000102836
| Domain | Start | End | E-Value | Type |
|---|
|
Blast:CA
|
18 |
66 |
5e-20 |
BLAST |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.0%
- 20x: 94.7%
|
| Validation Efficiency |
91% (43/47) |
| 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: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A730013G03Rik |
T |
A |
1: 192,515,731 (GRCm39) |
|
noncoding transcript |
Het |
| Adgrg6 |
A |
G |
10: 14,285,507 (GRCm39) |
S1160P |
probably damaging |
Het |
| Akt1 |
C |
T |
12: 112,625,567 (GRCm39) |
R144H |
probably benign |
Het |
| Arrdc3 |
T |
C |
13: 81,037,182 (GRCm39) |
|
probably benign |
Het |
| Asxl2 |
T |
A |
12: 3,551,774 (GRCm39) |
V1172E |
possibly damaging |
Het |
| Atp9a |
C |
T |
2: 168,523,917 (GRCm39) |
A242T |
possibly damaging |
Het |
| C2cd3 |
C |
T |
7: 100,023,684 (GRCm39) |
T90I |
probably damaging |
Het |
| C4bp |
A |
G |
1: 130,570,692 (GRCm39) |
S295P |
probably benign |
Het |
| Cdkl2 |
G |
A |
5: 92,168,168 (GRCm39) |
T342I |
probably benign |
Het |
| Cep131 |
T |
C |
11: 119,955,645 (GRCm39) |
E1025G |
probably damaging |
Het |
| Crot |
T |
C |
5: 9,023,643 (GRCm39) |
H415R |
probably damaging |
Het |
| Cyp17a1 |
A |
G |
19: 46,656,462 (GRCm39) |
F411L |
probably damaging |
Het |
| Dgkb |
G |
T |
12: 38,234,952 (GRCm39) |
G439V |
probably damaging |
Het |
| Dgkh |
A |
G |
14: 78,865,523 (GRCm39) |
V20A |
probably damaging |
Het |
| Dipk1a |
T |
C |
5: 108,072,500 (GRCm39) |
Y52C |
probably damaging |
Het |
| Dysf |
A |
G |
6: 84,182,854 (GRCm39) |
N2035S |
probably damaging |
Het |
| Fzd1 |
A |
G |
5: 4,805,777 (GRCm39) |
Y602H |
probably damaging |
Het |
| Gm38706 |
C |
A |
6: 130,460,273 (GRCm39) |
|
noncoding transcript |
Het |
| Hmmr |
T |
C |
11: 40,606,148 (GRCm39) |
Q274R |
probably damaging |
Het |
| Homer3 |
G |
A |
8: 70,742,793 (GRCm39) |
|
probably null |
Het |
| Igsf9b |
A |
G |
9: 27,245,548 (GRCm39) |
T1172A |
probably benign |
Het |
| Klf5 |
C |
T |
14: 99,539,666 (GRCm39) |
R360C |
probably damaging |
Het |
| Lrat |
A |
G |
3: 82,804,293 (GRCm39) |
M228T |
probably damaging |
Het |
| Mms19 |
A |
T |
19: 41,952,372 (GRCm39) |
M119K |
possibly damaging |
Het |
| Myo3a |
A |
T |
2: 22,490,149 (GRCm39) |
K565N |
probably damaging |
Het |
| Or10n1 |
A |
T |
9: 39,525,294 (GRCm39) |
I144L |
probably benign |
Het |
| Or1ad6 |
C |
T |
11: 50,860,690 (GRCm39) |
P282S |
probably damaging |
Het |
| Or3a1d |
T |
C |
11: 74,237,588 (GRCm39) |
D274G |
probably benign |
Het |
| Pcdhga3 |
A |
G |
18: 37,808,938 (GRCm39) |
R464G |
probably damaging |
Het |
| Plxna2 |
C |
T |
1: 194,431,625 (GRCm39) |
S538F |
probably damaging |
Het |
| Pramel42 |
T |
A |
5: 94,685,702 (GRCm39) |
I454K |
probably damaging |
Het |
| Rnf13 |
A |
C |
3: 57,728,010 (GRCm39) |
K230T |
probably damaging |
Het |
| Sema6d |
A |
G |
2: 124,505,979 (GRCm39) |
M596V |
probably damaging |
Het |
| Slc25a25 |
T |
C |
2: 32,320,621 (GRCm39) |
K47E |
probably benign |
Het |
| Sptbn1 |
C |
T |
11: 30,089,114 (GRCm39) |
R716H |
possibly damaging |
Het |
| Ssx2ip |
G |
A |
3: 146,132,186 (GRCm39) |
V216I |
probably benign |
Het |
| Tatdn2 |
T |
G |
6: 113,679,501 (GRCm39) |
|
probably null |
Het |
| Tmprss6 |
A |
G |
15: 78,337,039 (GRCm39) |
Y356H |
probably damaging |
Het |
| Ttn |
A |
G |
2: 76,687,210 (GRCm39) |
|
probably benign |
Het |
| Umod |
A |
G |
7: 119,065,279 (GRCm39) |
|
probably null |
Het |
| Vmn2r93 |
T |
A |
17: 18,524,312 (GRCm39) |
I102K |
possibly damaging |
Het |
| Zdhhc6 |
T |
C |
19: 55,291,169 (GRCm39) |
I349V |
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 |
|
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 |
PCR Primer
(F):5'- GTCTACCACCGAGTTCCATC -3'
(R):5'- CATTCTGCAGATTTACCTCCAGAAG -3'
Sequencing Primer
(F):5'- TACCACCGAGTTCCATCTACCAC -3'
(R):5'- TTGGACGCCACCCTGAACAG -3'
|
| Posted On |
2015-07-21 |
Incidental Mutation