Incidental Mutation 'R6720:Pcdha9'
| ID |
529563 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha9
|
| Ensembl Gene |
ENSMUSG00000103770 |
| Gene Name |
protocadherin alpha 9 |
| Synonyms |
|
| MMRRC Submission |
044838-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.694)
|
| Stock # |
R6720 (G1)
|
| Quality Score |
215.009 |
|
Status
|
Not validated
|
| Chromosome |
18 |
| Chromosomal Location |
36997880-37187657 bp(+) (GRCm38) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 36998069 bp (GRCm38)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Proline
at position 64
(S64P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000111323
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000070797]
[ENSMUST00000115659]
[ENSMUST00000115661]
[ENSMUST00000115662]
[ENSMUST00000192168]
[ENSMUST00000192295]
[ENSMUST00000192503]
[ENSMUST00000192512]
[ENSMUST00000192631]
[ENSMUST00000193389]
[ENSMUST00000194544]
[ENSMUST00000193839]
[ENSMUST00000195590]
[ENSMUST00000193777]
[ENSMUST00000194751]
[ENSMUST00000194038]
|
| AlphaFold |
Q91Y11 |
| 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 damaging
Transcript: ENSMUST00000115659
AA Change: S64P
PolyPhen 2
Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000111323
Gene: ENSMUSG00000103770
AA Change: S64P
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
44 |
51 |
N/A |
INTRINSIC |
|
CA
|
75 |
161 |
2.46e-2 |
SMART |
|
CA
|
185 |
270 |
8.1e-20 |
SMART |
|
CA
|
294 |
378 |
1.69e-22 |
SMART |
|
CA
|
402 |
483 |
1.52e-24 |
SMART |
|
CA
|
507 |
593 |
5.68e-24 |
SMART |
|
CA
|
624 |
705 |
6.69e-12 |
SMART |
|
transmembrane domain
|
727 |
749 |
N/A |
INTRINSIC |
|
Pfam:Cadherin_tail
|
828 |
962 |
5.6e-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 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: ENSMUST00000193389
|
| SMART Domains |
Protein: ENSMUSP00000141459
Gene: ENSMUSG00000103707
| 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: 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: ENSMUST00000193984
|
| 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: 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: ENSMUST00000193777
|
| SMART Domains |
Protein: ENSMUSP00000141587
Gene: ENSMUSG00000103707
| 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: 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: ENSMUST00000194038
|
| SMART Domains |
Protein: ENSMUSP00000142159
Gene: ENSMUSG00000103800
| Domain | Start | End | E-Value | Type |
|---|
|
CA
|
20 |
131 |
6.34e-2 |
SMART |
|
CA
|
155 |
240 |
4.27e-19 |
SMART |
|
CA
|
264 |
348 |
2.04e-25 |
SMART |
|
CA
|
372 |
453 |
2.84e-24 |
SMART |
|
CA
|
477 |
563 |
9.88e-24 |
SMART |
|
CA
|
594 |
676 |
8.62e-15 |
SMART |
|
transmembrane domain
|
699 |
721 |
N/A |
INTRINSIC |
|
low complexity region
|
914 |
938 |
N/A |
INTRINSIC |
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.5%
- 10x: 97.7%
- 20x: 93.6%
|
| Validation Efficiency |
98% (50/51) |
| 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: 50 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700013G24Rik |
G |
A |
4: 137,454,686 |
E51K |
possibly damaging |
Het |
| Abca1 |
A |
C |
4: 53,083,733 |
L700R |
probably damaging |
Het |
| Arpc1a |
C |
A |
5: 145,101,222 |
|
probably null |
Het |
| Baz2b |
G |
T |
2: 59,924,890 |
P241Q |
probably damaging |
Het |
| Cd6 |
T |
A |
19: 10,794,609 |
T414S |
probably benign |
Het |
| Ces2b |
A |
T |
8: 104,836,869 |
E409D |
probably benign |
Het |
| Cfap54 |
A |
G |
10: 92,821,119 |
Y3024H |
probably benign |
Het |
| Chrm1 |
A |
G |
19: 8,678,548 |
T206A |
probably benign |
Het |
| Clptm1l |
T |
C |
13: 73,618,516 |
W512R |
probably damaging |
Het |
| Col15a1 |
T |
A |
4: 47,247,552 |
|
probably null |
Het |
| Cox15 |
A |
G |
19: 43,736,789 |
S392P |
probably damaging |
Het |
| Cr2 |
T |
C |
1: 195,155,200 |
M1197V |
probably damaging |
Het |
| Ddx60 |
A |
G |
8: 62,000,689 |
K1281E |
probably benign |
Het |
| Dnah11 |
A |
G |
12: 118,045,646 |
F2094L |
probably damaging |
Het |
| Ear2 |
T |
A |
14: 44,102,959 |
C25S |
probably damaging |
Het |
| Ect2l |
T |
C |
10: 18,140,264 |
D802G |
probably damaging |
Het |
| Eftud2 |
G |
A |
11: 102,838,623 |
Q84* |
probably null |
Het |
| Eif4g3 |
T |
A |
4: 138,175,832 |
|
probably null |
Het |
| Ephb2 |
T |
C |
4: 136,657,502 |
D866G |
probably damaging |
Het |
| Fam129b |
T |
A |
2: 32,905,826 |
V22D |
probably damaging |
Het |
| Farsb |
A |
G |
1: 78,472,497 |
M99T |
probably damaging |
Het |
| Foxs1 |
T |
A |
2: 152,932,720 |
S138C |
probably damaging |
Het |
| Frem1 |
T |
G |
4: 83,013,832 |
S211R |
probably damaging |
Het |
| Gm19410 |
G |
A |
8: 35,807,576 |
R1517Q |
probably benign |
Het |
| Gria2 |
T |
C |
3: 80,802,304 |
I27M |
probably benign |
Het |
| H2-Q7 |
A |
G |
17: 35,442,678 |
E299G |
probably benign |
Het |
| Hao2 |
T |
G |
3: 98,877,135 |
I305L |
probably benign |
Het |
| Hectd4 |
C |
T |
5: 121,307,381 |
Q122* |
probably null |
Het |
| Hivep1 |
T |
A |
13: 42,164,284 |
C2079S |
probably damaging |
Het |
| Hoxb1 |
C |
A |
11: 96,366,987 |
Q248K |
probably damaging |
Het |
| Hspb6 |
A |
G |
7: 30,554,347 |
D95G |
probably benign |
Het |
| Ighv5-2 |
T |
A |
12: 113,578,506 |
R117S |
probably damaging |
Het |
| Ino80d |
A |
C |
1: 63,058,610 |
S708R |
probably damaging |
Het |
| Lman1l |
A |
G |
9: 57,614,072 |
|
probably null |
Het |
| Mmp15 |
A |
G |
8: 95,365,314 |
N51D |
probably benign |
Het |
| Naip1 |
T |
C |
13: 100,423,077 |
M1140V |
probably benign |
Het |
| Olfr1053 |
A |
G |
2: 86,315,065 |
S74P |
probably damaging |
Het |
| Olfr1373 |
A |
G |
11: 52,144,693 |
V279A |
probably benign |
Het |
| Olfr397 |
A |
G |
11: 73,965,465 |
N286D |
probably damaging |
Het |
| Olfr890 |
T |
A |
9: 38,143,153 |
M1K |
probably null |
Het |
| Pard3b |
A |
T |
1: 62,159,470 |
N239I |
probably damaging |
Het |
| Parvb |
C |
T |
15: 84,297,979 |
R237W |
probably damaging |
Het |
| Pdcd1 |
T |
C |
1: 94,041,389 |
N68S |
probably benign |
Het |
| Pi4ka |
G |
T |
16: 17,326,052 |
|
probably null |
Het |
| Plekha4 |
A |
T |
7: 45,540,886 |
D359V |
possibly damaging |
Het |
| Serpinb13 |
A |
G |
1: 106,994,062 |
I78V |
probably benign |
Het |
| Slc39a7 |
T |
A |
17: 34,030,108 |
T269S |
probably benign |
Het |
| Sltm |
T |
G |
9: 70,573,710 |
D281E |
probably damaging |
Het |
| Zfp708 |
T |
C |
13: 67,071,432 |
Y76C |
probably damaging |
Het |
| Zfp990 |
T |
A |
4: 145,536,927 |
V165D |
possibly damaging |
Het |
|
| Other mutations in Pcdha9 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
R0761:Pcdha9
|
UTSW |
18 |
36999963 |
nonsense |
probably null |
|
|
R2985:Pcdha9
|
UTSW |
18 |
36998202 |
missense |
possibly damaging |
0.88 |
|
R3926:Pcdha9
|
UTSW |
18 |
36999412 |
missense |
probably damaging |
1.00 |
|
R4049:Pcdha9
|
UTSW |
18 |
36997942 |
missense |
probably benign |
0.16 |
|
R4409:Pcdha9
|
UTSW |
18 |
36999145 |
missense |
probably benign |
0.12 |
|
R4816:Pcdha9
|
UTSW |
18 |
36999458 |
missense |
probably damaging |
1.00 |
|
R4905:Pcdha9
|
UTSW |
18 |
36998892 |
missense |
probably damaging |
0.96 |
|
R4991:Pcdha9
|
UTSW |
18 |
36998345 |
missense |
probably damaging |
0.99 |
|
R5484:Pcdha9
|
UTSW |
18 |
36998103 |
missense |
probably damaging |
1.00 |
|
R5487:Pcdha9
|
UTSW |
18 |
36999650 |
missense |
probably damaging |
1.00 |
|
R5617:Pcdha9
|
UTSW |
18 |
36998816 |
missense |
probably benign |
0.03 |
|
R5637:Pcdha9
|
UTSW |
18 |
36998373 |
missense |
probably benign |
0.00 |
|
R5694:Pcdha9
|
UTSW |
18 |
36998372 |
missense |
probably benign |
0.00 |
|
R5975:Pcdha9
|
UTSW |
18 |
36999111 |
missense |
probably benign |
0.00 |
|
R6089:Pcdha9
|
UTSW |
18 |
36998498 |
missense |
probably benign |
0.00 |
|
R6176:Pcdha9
|
UTSW |
18 |
36998931 |
missense |
probably benign |
0.24 |
|
R6220:Pcdha9
|
UTSW |
18 |
36998478 |
missense |
probably damaging |
1.00 |
|
R6238:Pcdha9
|
UTSW |
18 |
36998975 |
missense |
probably benign |
0.43 |
|
R6391:Pcdha9
|
UTSW |
18 |
36997919 |
missense |
probably benign |
0.12 |
|
R6622:Pcdha9
|
UTSW |
18 |
36998654 |
missense |
possibly damaging |
0.84 |
|
R7239:Pcdha9
|
UTSW |
18 |
36998498 |
missense |
probably benign |
0.06 |
|
R7624:Pcdha9
|
UTSW |
18 |
36999796 |
nonsense |
probably null |
|
|
R7721:Pcdha9
|
UTSW |
18 |
36999636 |
missense |
probably benign |
|
|
R8211:Pcdha9
|
UTSW |
18 |
36998859 |
missense |
possibly damaging |
0.56 |
|
R8483:Pcdha9
|
UTSW |
18 |
36998583 |
missense |
probably benign |
0.01 |
|
R8778:Pcdha9
|
UTSW |
18 |
36999191 |
missense |
possibly damaging |
0.65 |
|
R8946:Pcdha9
|
UTSW |
18 |
36998493 |
missense |
possibly damaging |
0.92 |
|
R8963:Pcdha9
|
UTSW |
18 |
36998697 |
missense |
probably benign |
0.43 |
|
R8987:Pcdha9
|
UTSW |
18 |
36999945 |
missense |
probably benign |
0.22 |
|
R9227:Pcdha9
|
UTSW |
18 |
36998901 |
missense |
probably damaging |
1.00 |
|
R9287:Pcdha9
|
UTSW |
18 |
36999228 |
missense |
probably benign |
0.00 |
|
R9439:Pcdha9
|
UTSW |
18 |
36998474 |
missense |
probably benign |
0.07 |
|
Z1177:Pcdha9
|
UTSW |
18 |
36998214 |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- AGCTACGTTCGGAGATCTCG -3'
(R):5'- GGTCGATCCGAGAATTCACAAAC -3'
Sequencing Primer
(F):5'- CGGAGATCTCGGCGTTTC -3'
(R):5'- CAAAATGCCATTCTGAAGATTTACC -3'
|
| Posted On |
2018-08-01 |
Incidental Mutation