Incidental Mutation 'R2985:Pcdha9'
| ID |
477434 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha9
|
| Ensembl Gene |
ENSMUSG00000103770 |
| Gene Name |
protocadherin alpha 9 |
| Synonyms |
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.684)
|
| Stock # |
R2985 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
18 |
| Chromosomal Location |
37130933-37320710 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 37131255 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Serine
at position 108
(N108S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000111323
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000070797]
[ENSMUST00000115659]
[ENSMUST00000115661]
[ENSMUST00000115662]
[ENSMUST00000192168]
[ENSMUST00000192295]
[ENSMUST00000192503]
[ENSMUST00000193389]
[ENSMUST00000194038]
[ENSMUST00000193839]
[ENSMUST00000195590]
[ENSMUST00000192512]
[ENSMUST00000193777]
[ENSMUST00000194544]
[ENSMUST00000194751]
[ENSMUST00000192631]
|
| 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 |
possibly damaging
Transcript: ENSMUST00000115659
AA Change: N108S
PolyPhen 2
Score 0.884 (Sensitivity: 0.82; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000111323
Gene: ENSMUSG00000103770
AA Change: N108S
| 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: 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: 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 |
|
| 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: 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: 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: 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: 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 |
|
| Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.7%
- 10x: 97.2%
- 20x: 94.7%
|
| 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: 18 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Bahd1 |
G |
A |
2: 118,753,004 (GRCm39) |
R757H |
probably damaging |
Het |
| Ccdc83 |
A |
G |
7: 89,885,575 (GRCm39) |
|
probably benign |
Het |
| Chil4 |
G |
A |
3: 106,111,043 (GRCm39) |
P284S |
possibly damaging |
Het |
| Cul1 |
T |
A |
6: 47,479,441 (GRCm39) |
F236I |
probably damaging |
Het |
| Etl4 |
T |
C |
2: 20,786,660 (GRCm39) |
V470A |
probably damaging |
Het |
| Fndc1 |
T |
C |
17: 7,975,155 (GRCm39) |
E1428G |
possibly damaging |
Het |
| Gal3st1 |
A |
G |
11: 3,948,618 (GRCm39) |
Y275C |
probably damaging |
Het |
| Jakmip2 |
G |
A |
18: 43,704,246 (GRCm39) |
T366I |
possibly damaging |
Het |
| Mfsd13a |
C |
T |
19: 46,360,431 (GRCm39) |
R328C |
probably damaging |
Het |
| Obscn |
A |
G |
11: 59,023,915 (GRCm39) |
F585S |
probably damaging |
Het |
| Or8b56 |
G |
A |
9: 38,739,406 (GRCm39) |
V140I |
probably benign |
Het |
| Oxld1 |
T |
C |
11: 120,347,862 (GRCm39) |
T112A |
probably benign |
Het |
| Pkd1l2 |
T |
C |
8: 117,792,290 (GRCm39) |
S501G |
probably benign |
Het |
| Pls1 |
G |
A |
9: 95,667,635 (GRCm39) |
T91M |
possibly damaging |
Het |
| Prr12 |
G |
C |
7: 44,695,436 (GRCm39) |
S1343R |
unknown |
Het |
| Trpm5 |
G |
T |
7: 142,636,675 (GRCm39) |
L421I |
probably damaging |
Het |
| Ttn |
A |
T |
2: 76,574,618 (GRCm39) |
V25425E |
probably damaging |
Het |
| Zfp112 |
A |
G |
7: 23,821,720 (GRCm39) |
D20G |
probably benign |
Het |
|
| Other mutations in Pcdha9 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
R0761:Pcdha9
|
UTSW |
18 |
37,133,016 (GRCm39) |
nonsense |
probably null |
|
|
R3926:Pcdha9
|
UTSW |
18 |
37,132,465 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4049:Pcdha9
|
UTSW |
18 |
37,130,995 (GRCm39) |
missense |
probably benign |
0.16 |
|
R4409:Pcdha9
|
UTSW |
18 |
37,132,198 (GRCm39) |
missense |
probably benign |
0.12 |
|
R4816:Pcdha9
|
UTSW |
18 |
37,132,511 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4905:Pcdha9
|
UTSW |
18 |
37,131,945 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R4991:Pcdha9
|
UTSW |
18 |
37,131,398 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5484:Pcdha9
|
UTSW |
18 |
37,131,156 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5487:Pcdha9
|
UTSW |
18 |
37,132,703 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5617:Pcdha9
|
UTSW |
18 |
37,131,869 (GRCm39) |
missense |
probably benign |
0.03 |
|
R5637:Pcdha9
|
UTSW |
18 |
37,131,426 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5694:Pcdha9
|
UTSW |
18 |
37,131,425 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5975:Pcdha9
|
UTSW |
18 |
37,132,164 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6089:Pcdha9
|
UTSW |
18 |
37,131,551 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6176:Pcdha9
|
UTSW |
18 |
37,131,984 (GRCm39) |
missense |
probably benign |
0.24 |
|
R6220:Pcdha9
|
UTSW |
18 |
37,131,531 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6238:Pcdha9
|
UTSW |
18 |
37,132,028 (GRCm39) |
missense |
probably benign |
0.43 |
|
R6391:Pcdha9
|
UTSW |
18 |
37,130,972 (GRCm39) |
missense |
probably benign |
0.12 |
|
R6622:Pcdha9
|
UTSW |
18 |
37,131,707 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
R6720:Pcdha9
|
UTSW |
18 |
37,131,122 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7239:Pcdha9
|
UTSW |
18 |
37,131,551 (GRCm39) |
missense |
probably benign |
0.06 |
|
R7624:Pcdha9
|
UTSW |
18 |
37,132,849 (GRCm39) |
nonsense |
probably null |
|
|
R7721:Pcdha9
|
UTSW |
18 |
37,132,689 (GRCm39) |
missense |
probably benign |
|
|
R8211:Pcdha9
|
UTSW |
18 |
37,131,912 (GRCm39) |
missense |
possibly damaging |
0.56 |
|
R8483:Pcdha9
|
UTSW |
18 |
37,131,636 (GRCm39) |
missense |
probably benign |
0.01 |
|
R8778:Pcdha9
|
UTSW |
18 |
37,132,244 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
R8946:Pcdha9
|
UTSW |
18 |
37,131,546 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R8963:Pcdha9
|
UTSW |
18 |
37,131,750 (GRCm39) |
missense |
probably benign |
0.43 |
|
R8987:Pcdha9
|
UTSW |
18 |
37,132,998 (GRCm39) |
missense |
probably benign |
0.22 |
|
R9227:Pcdha9
|
UTSW |
18 |
37,131,954 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9287:Pcdha9
|
UTSW |
18 |
37,132,281 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9439:Pcdha9
|
UTSW |
18 |
37,131,527 (GRCm39) |
missense |
probably benign |
0.07 |
|
Z1177:Pcdha9
|
UTSW |
18 |
37,131,267 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
|
| Posted On |
2017-05-15 |
Incidental Mutation