Incidental Mutation 'R3895:Pcdh9'
| ID |
310514 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdh9
|
| Ensembl Gene |
ENSMUSG00000055421 |
| Gene Name |
protocadherin 9 |
| Synonyms |
C630029H24Rik, LOC382930, A730003J17Rik, 1500001L12Rik, C530050I23Rik |
| MMRRC Submission |
040806-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.166)
|
| Stock # |
R3895 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
14 |
| Chromosomal Location |
93250846-94128115 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 94124974 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Methionine
at position 399
(V399M)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000141759
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000068992]
[ENSMUST00000192221]
[ENSMUST00000193901]
[ENSMUST00000194056]
[ENSMUST00000195376]
[ENSMUST00000195826]
|
| AlphaFold |
F8VPK8 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000068992
AA Change: V399M
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000070935
Gene: ENSMUSG00000055421
AA Change: V399M
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
CA
|
49 |
140 |
8.37e-3 |
SMART |
|
CA
|
164 |
250 |
1.01e-20 |
SMART |
|
CA
|
274 |
356 |
2.34e-25 |
SMART |
|
CA
|
386 |
467 |
2.14e-19 |
SMART |
|
CA
|
491 |
570 |
4.27e-28 |
SMART |
|
CA
|
594 |
673 |
2.45e-28 |
SMART |
|
CA
|
700 |
782 |
1.01e-6 |
SMART |
|
transmembrane domain
|
814 |
836 |
N/A |
INTRINSIC |
|
low complexity region
|
858 |
883 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000192221
AA Change: V276M
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000142260
Gene: ENSMUSG00000055421
AA Change: V276M
| Domain | Start | End | E-Value | Type |
|---|
|
CA
|
41 |
127 |
1.01e-20 |
SMART |
|
CA
|
151 |
233 |
2.34e-25 |
SMART |
|
CA
|
263 |
344 |
2.14e-19 |
SMART |
|
CA
|
368 |
447 |
4.27e-28 |
SMART |
|
CA
|
471 |
550 |
2.45e-28 |
SMART |
|
CA
|
577 |
659 |
1.01e-6 |
SMART |
|
transmembrane domain
|
691 |
713 |
N/A |
INTRINSIC |
|
low complexity region
|
735 |
760 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000192817
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000193901
AA Change: V399M
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000141759
Gene: ENSMUSG00000055421
AA Change: V399M
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
CA
|
49 |
140 |
8.37e-3 |
SMART |
|
CA
|
164 |
250 |
1.01e-20 |
SMART |
|
CA
|
274 |
356 |
2.34e-25 |
SMART |
|
CA
|
386 |
467 |
2.14e-19 |
SMART |
|
CA
|
491 |
570 |
4.27e-28 |
SMART |
|
CA
|
594 |
673 |
2.45e-28 |
SMART |
|
CA
|
700 |
782 |
1.01e-6 |
SMART |
|
transmembrane domain
|
814 |
836 |
N/A |
INTRINSIC |
|
low complexity region
|
858 |
883 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000194056
AA Change: V399M
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000141602
Gene: ENSMUSG00000055421
AA Change: V399M
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
CA
|
49 |
140 |
4.1e-5 |
SMART |
|
CA
|
164 |
250 |
4.8e-23 |
SMART |
|
CA
|
274 |
356 |
1.2e-27 |
SMART |
|
CA
|
386 |
467 |
1.1e-21 |
SMART |
|
CA
|
491 |
570 |
2e-30 |
SMART |
|
CA
|
594 |
673 |
1.2e-30 |
SMART |
|
CA
|
700 |
782 |
4.9e-9 |
SMART |
|
transmembrane domain
|
814 |
836 |
N/A |
INTRINSIC |
|
low complexity region
|
860 |
873 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000194129
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000195376
AA Change: V399M
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000142224
Gene: ENSMUSG00000055421
AA Change: V399M
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
CA
|
49 |
140 |
4.1e-5 |
SMART |
|
CA
|
164 |
250 |
4.8e-23 |
SMART |
|
CA
|
274 |
356 |
1.2e-27 |
SMART |
|
CA
|
386 |
467 |
1.1e-21 |
SMART |
|
CA
|
491 |
570 |
2e-30 |
SMART |
|
CA
|
594 |
673 |
1.2e-30 |
SMART |
|
CA
|
700 |
782 |
4.9e-9 |
SMART |
|
transmembrane domain
|
814 |
836 |
N/A |
INTRINSIC |
|
low complexity region
|
858 |
883 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000195826
AA Change: V399M
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000141396
Gene: ENSMUSG00000055421
AA Change: V399M
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
CA
|
49 |
140 |
8.37e-3 |
SMART |
|
CA
|
164 |
250 |
1.01e-20 |
SMART |
|
CA
|
274 |
356 |
2.34e-25 |
SMART |
|
CA
|
386 |
467 |
2.14e-19 |
SMART |
|
CA
|
491 |
570 |
4.27e-28 |
SMART |
|
CA
|
594 |
673 |
2.45e-28 |
SMART |
|
CA
|
700 |
782 |
1.01e-6 |
SMART |
|
transmembrane domain
|
814 |
836 |
N/A |
INTRINSIC |
|
low complexity region
|
858 |
883 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.3385 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.4%
|
| Validation Efficiency |
96% (45/47) |
| MGI Phenotype |
FUNCTION: This gene encodes a member of the protocadherin family, and cadherin superfamily, of transmembrane proteins containing cadherin domains. These proteins mediate cell adhesion in neural tissues in the presence of calcium. The encoded protein may be involved in signaling at neuronal synaptic junctions. Sharing a characteristic with other protocadherin genes, this gene has a notably large exon that encodes multiple cadherin domains and a transmembrane region. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2012]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit impaired long-term social and bject recognition and sensorimotor development. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 42 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acoxl |
T |
C |
2: 127,814,445 (GRCm39) |
|
probably benign |
Het |
| C6 |
T |
C |
15: 4,837,952 (GRCm39) |
V854A |
probably benign |
Het |
| Ccnd1 |
T |
C |
7: 144,491,631 (GRCm39) |
E136G |
probably damaging |
Het |
| CK137956 |
A |
T |
4: 127,840,441 (GRCm39) |
F422I |
probably benign |
Het |
| Csta1 |
T |
C |
16: 35,951,402 (GRCm39) |
T7A |
probably benign |
Het |
| Dock8 |
A |
G |
19: 25,028,865 (GRCm39) |
E23G |
probably benign |
Het |
| Fbxo8 |
A |
T |
8: 57,044,556 (GRCm39) |
R286S |
probably damaging |
Het |
| Gm12258 |
T |
G |
11: 58,749,375 (GRCm39) |
Y183* |
probably null |
Het |
| Gvin-ps6 |
T |
A |
7: 106,022,621 (GRCm39) |
H127L |
probably damaging |
Het |
| Hectd3 |
A |
G |
4: 116,853,286 (GRCm39) |
D171G |
probably damaging |
Het |
| Hoxd11 |
C |
T |
2: 74,513,136 (GRCm39) |
R134W |
probably damaging |
Het |
| Ighg2c |
T |
C |
12: 113,251,278 (GRCm39) |
T246A |
unknown |
Het |
| Ints6 |
T |
C |
14: 62,934,060 (GRCm39) |
I816V |
probably damaging |
Het |
| Lrp4 |
G |
A |
2: 91,304,294 (GRCm39) |
G158S |
probably damaging |
Het |
| Mast1 |
G |
A |
8: 85,662,352 (GRCm39) |
P52L |
probably damaging |
Het |
| Med13l |
A |
G |
5: 118,899,388 (GRCm39) |
D2148G |
probably null |
Het |
| Med24 |
A |
G |
11: 98,597,214 (GRCm39) |
S889P |
probably benign |
Het |
| Mgam |
T |
A |
6: 40,736,054 (GRCm39) |
M851K |
probably damaging |
Het |
| Mkln1 |
T |
A |
6: 31,484,602 (GRCm39) |
L710H |
probably damaging |
Het |
| Morf4l1 |
A |
T |
9: 89,976,501 (GRCm39) |
F276I |
possibly damaging |
Het |
| Mslnl |
G |
A |
17: 25,961,908 (GRCm39) |
V128M |
probably damaging |
Het |
| Myt1 |
T |
A |
2: 181,461,863 (GRCm39) |
S574R |
probably damaging |
Het |
| Nol11 |
C |
A |
11: 107,059,173 (GRCm39) |
V644F |
probably damaging |
Het |
| Nusap1 |
C |
A |
2: 119,458,172 (GRCm39) |
Q103K |
possibly damaging |
Het |
| Ovgp1 |
A |
G |
3: 105,893,912 (GRCm39) |
|
probably benign |
Het |
| Plekhh1 |
T |
C |
12: 79,102,006 (GRCm39) |
S359P |
probably benign |
Het |
| Prg4 |
G |
C |
1: 150,330,510 (GRCm39) |
|
probably benign |
Het |
| Ptpn14 |
C |
T |
1: 189,582,743 (GRCm39) |
A530V |
probably benign |
Het |
| Rho |
A |
G |
6: 115,910,863 (GRCm39) |
Y136C |
probably damaging |
Het |
| Rps3 |
C |
T |
7: 99,129,103 (GRCm39) |
R173H |
probably benign |
Het |
| Rufy4 |
T |
C |
1: 74,186,822 (GRCm39) |
C537R |
probably damaging |
Het |
| Sall2 |
T |
C |
14: 52,551,504 (GRCm39) |
N564D |
probably damaging |
Het |
| Sart3 |
G |
A |
5: 113,890,488 (GRCm39) |
R452* |
probably null |
Het |
| Sbf2 |
T |
C |
7: 110,046,298 (GRCm39) |
I300V |
probably damaging |
Het |
| Sgo2b |
A |
T |
8: 64,381,767 (GRCm39) |
V355E |
possibly damaging |
Het |
| Slc22a5 |
T |
C |
11: 53,756,651 (GRCm39) |
K553R |
possibly damaging |
Het |
| Syne1 |
A |
G |
10: 5,355,456 (GRCm39) |
V375A |
probably damaging |
Het |
| Trafd1 |
T |
C |
5: 121,516,804 (GRCm39) |
E28G |
probably benign |
Het |
| Tsc2 |
T |
C |
17: 24,818,786 (GRCm39) |
K1292R |
probably damaging |
Het |
| Twnk |
A |
G |
19: 44,995,890 (GRCm39) |
T108A |
probably damaging |
Het |
| Unc13c |
A |
T |
9: 73,840,805 (GRCm39) |
H15Q |
probably benign |
Het |
| Vps16 |
T |
C |
2: 130,280,596 (GRCm39) |
S208P |
possibly damaging |
Het |
|
| Other mutations in Pcdh9 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00482:Pcdh9
|
APN |
14 |
93,564,130 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02183:Pcdh9
|
APN |
14 |
94,123,720 (GRCm39) |
missense |
probably benign |
0.01 |
|
IGL02244:Pcdh9
|
APN |
14 |
93,564,204 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02571:Pcdh9
|
APN |
14 |
93,798,023 (GRCm39) |
splice site |
probably benign |
|
|
IGL03018:Pcdh9
|
APN |
14 |
93,253,012 (GRCm39) |
missense |
probably null |
|
|
I1329:Pcdh9
|
UTSW |
14 |
94,123,645 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0027:Pcdh9
|
UTSW |
14 |
94,126,081 (GRCm39) |
missense |
probably null |
0.99 |
|
R0027:Pcdh9
|
UTSW |
14 |
94,126,081 (GRCm39) |
missense |
probably null |
0.99 |
|
R0477:Pcdh9
|
UTSW |
14 |
94,125,114 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0499:Pcdh9
|
UTSW |
14 |
94,123,671 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0787:Pcdh9
|
UTSW |
14 |
94,124,193 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R1205:Pcdh9
|
UTSW |
14 |
94,123,501 (GRCm39) |
missense |
probably benign |
0.01 |
|
R1616:Pcdh9
|
UTSW |
14 |
94,124,405 (GRCm39) |
nonsense |
probably null |
|
|
R1620:Pcdh9
|
UTSW |
14 |
94,125,741 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1622:Pcdh9
|
UTSW |
14 |
94,123,311 (GRCm39) |
missense |
probably benign |
0.03 |
|
R1708:Pcdh9
|
UTSW |
14 |
94,125,741 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1721:Pcdh9
|
UTSW |
14 |
94,125,471 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1753:Pcdh9
|
UTSW |
14 |
94,124,661 (GRCm39) |
missense |
probably benign |
0.33 |
|
R1799:Pcdh9
|
UTSW |
14 |
94,126,107 (GRCm39) |
missense |
probably benign |
0.36 |
|
R1867:Pcdh9
|
UTSW |
14 |
94,125,471 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1987:Pcdh9
|
UTSW |
14 |
94,125,741 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1988:Pcdh9
|
UTSW |
14 |
94,125,741 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2444:Pcdh9
|
UTSW |
14 |
94,124,227 (GRCm39) |
missense |
probably benign |
0.10 |
|
R3926:Pcdh9
|
UTSW |
14 |
94,124,246 (GRCm39) |
nonsense |
probably null |
|
|
R4166:Pcdh9
|
UTSW |
14 |
94,124,956 (GRCm39) |
nonsense |
probably null |
|
|
R4429:Pcdh9
|
UTSW |
14 |
94,124,820 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R4589:Pcdh9
|
UTSW |
14 |
94,125,628 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4604:Pcdh9
|
UTSW |
14 |
94,124,616 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4607:Pcdh9
|
UTSW |
14 |
93,253,009 (GRCm39) |
missense |
probably benign |
0.08 |
|
R4621:Pcdh9
|
UTSW |
14 |
94,125,079 (GRCm39) |
missense |
probably benign |
0.12 |
|
R4624:Pcdh9
|
UTSW |
14 |
94,123,845 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4712:Pcdh9
|
UTSW |
14 |
94,126,067 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4788:Pcdh9
|
UTSW |
14 |
94,124,851 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4831:Pcdh9
|
UTSW |
14 |
94,125,377 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4883:Pcdh9
|
UTSW |
14 |
94,126,164 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
R5034:Pcdh9
|
UTSW |
14 |
93,564,285 (GRCm39) |
missense |
probably benign |
0.13 |
|
R5175:Pcdh9
|
UTSW |
14 |
94,125,879 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5637:Pcdh9
|
UTSW |
14 |
94,123,198 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R5743:Pcdh9
|
UTSW |
14 |
94,124,160 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5753:Pcdh9
|
UTSW |
14 |
94,125,597 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5770:Pcdh9
|
UTSW |
14 |
94,124,379 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5900:Pcdh9
|
UTSW |
14 |
93,564,156 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5986:Pcdh9
|
UTSW |
14 |
94,124,484 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6052:Pcdh9
|
UTSW |
14 |
94,123,282 (GRCm39) |
missense |
probably benign |
0.40 |
|
R6113:Pcdh9
|
UTSW |
14 |
94,124,544 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6223:Pcdh9
|
UTSW |
14 |
93,253,169 (GRCm39) |
missense |
probably benign |
0.18 |
|
R6415:Pcdh9
|
UTSW |
14 |
93,253,278 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
R6435:Pcdh9
|
UTSW |
14 |
94,125,280 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7064:Pcdh9
|
UTSW |
14 |
94,123,585 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7143:Pcdh9
|
UTSW |
14 |
94,125,708 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7219:Pcdh9
|
UTSW |
14 |
93,253,216 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
R7262:Pcdh9
|
UTSW |
14 |
93,253,141 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7354:Pcdh9
|
UTSW |
14 |
94,125,706 (GRCm39) |
missense |
probably benign |
0.28 |
|
R7369:Pcdh9
|
UTSW |
14 |
94,123,803 (GRCm39) |
missense |
possibly damaging |
0.67 |
|
R7427:Pcdh9
|
UTSW |
14 |
94,124,547 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7428:Pcdh9
|
UTSW |
14 |
94,124,547 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7780:Pcdh9
|
UTSW |
14 |
94,123,987 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R7870:Pcdh9
|
UTSW |
14 |
94,124,693 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R7921:Pcdh9
|
UTSW |
14 |
93,253,001 (GRCm39) |
missense |
probably benign |
|
|
R8052:Pcdh9
|
UTSW |
14 |
94,123,222 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8252:Pcdh9
|
UTSW |
14 |
94,126,086 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8671:Pcdh9
|
UTSW |
14 |
94,126,086 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8672:Pcdh9
|
UTSW |
14 |
94,124,529 (GRCm39) |
missense |
probably benign |
0.08 |
|
R8724:Pcdh9
|
UTSW |
14 |
94,124,583 (GRCm39) |
missense |
probably benign |
0.19 |
|
R8974:Pcdh9
|
UTSW |
14 |
94,125,113 (GRCm39) |
missense |
probably benign |
0.20 |
|
R9044:Pcdh9
|
UTSW |
14 |
94,124,247 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9486:Pcdh9
|
UTSW |
14 |
93,797,956 (GRCm39) |
missense |
possibly damaging |
0.73 |
|
R9534:Pcdh9
|
UTSW |
14 |
94,123,656 (GRCm39) |
missense |
probably damaging |
0.99 |
|
X0012:Pcdh9
|
UTSW |
14 |
94,124,080 (GRCm39) |
missense |
possibly damaging |
0.71 |
|
X0067:Pcdh9
|
UTSW |
14 |
93,564,285 (GRCm39) |
missense |
probably benign |
0.13 |
|
| Predicted Primers |
PCR Primer
(F):5'- CCAGGGCAGTCTGATTCAAAC -3'
(R):5'- GAGACAGCCATTCACAAAGTG -3'
Sequencing Primer
(F):5'- GCAGTCTGATTCAAACTGGGC -3'
(R):5'- CCATTCACAAAGTGACAGTGCTGG -3'
|
| Posted On |
2015-04-17 |
Incidental Mutation