Incidental Mutation 'R1882:Pcdh1'
| ID |
209211 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdh1
|
| Ensembl Gene |
ENSMUSG00000051375 |
| Gene Name |
protocadherin 1 |
| Synonyms |
2010005A06Rik |
| MMRRC Submission |
039903-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.365)
|
| Stock # |
R1882 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
38318967-38345023 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 38335895 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 247
(T247A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000125309
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000057185]
[ENSMUST00000159405]
[ENSMUST00000160721]
[ENSMUST00000161701]
[ENSMUST00000193828]
[ENSMUST00000194312]
|
| AlphaFold |
Q8CFX3 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000057185
AA Change: T247A
PolyPhen 2
Score 0.485 (Sensitivity: 0.88; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000055199
Gene: ENSMUSG00000051375
AA Change: T247A
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
33 |
N/A |
INTRINSIC |
|
Pfam:Cadherin_2
|
36 |
120 |
2e-8 |
PFAM |
|
CA
|
168 |
256 |
5.18e-18 |
SMART |
|
CA
|
280 |
363 |
5.68e-24 |
SMART |
|
CA
|
395 |
482 |
1.84e-23 |
SMART |
|
CA
|
506 |
588 |
2.99e-32 |
SMART |
|
CA
|
612 |
691 |
9.36e-25 |
SMART |
|
CA
|
717 |
798 |
9.9e-15 |
SMART |
|
transmembrane domain
|
830 |
852 |
N/A |
INTRINSIC |
|
low complexity region
|
876 |
903 |
N/A |
INTRINSIC |
|
low complexity region
|
951 |
964 |
N/A |
INTRINSIC |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000159405
AA Change: T247A
PolyPhen 2
Score 0.485 (Sensitivity: 0.88; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000125309
Gene: ENSMUSG00000051375
AA Change: T247A
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
33 |
N/A |
INTRINSIC |
|
Pfam:Cadherin_2
|
36 |
120 |
2e-8 |
PFAM |
|
CA
|
168 |
256 |
5.18e-18 |
SMART |
|
CA
|
280 |
363 |
5.68e-24 |
SMART |
|
CA
|
395 |
482 |
1.84e-23 |
SMART |
|
CA
|
506 |
588 |
2.99e-32 |
SMART |
|
CA
|
612 |
691 |
9.36e-25 |
SMART |
|
CA
|
717 |
798 |
9.9e-15 |
SMART |
|
transmembrane domain
|
830 |
852 |
N/A |
INTRINSIC |
|
low complexity region
|
876 |
903 |
N/A |
INTRINSIC |
|
low complexity region
|
951 |
964 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000160721
AA Change: T247A
PolyPhen 2
Score 0.058 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000124732
Gene: ENSMUSG00000051375
AA Change: T247A
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
33 |
N/A |
INTRINSIC |
|
Pfam:Cadherin_2
|
36 |
120 |
9.9e-10 |
PFAM |
|
CA
|
168 |
256 |
5.18e-18 |
SMART |
|
low complexity region
|
310 |
321 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000161701
AA Change: T108A
PolyPhen 2
Score 0.058 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000125576
Gene: ENSMUSG00000051375
AA Change: T108A
| Domain | Start | End | E-Value | Type |
|---|
|
CA
|
29 |
117 |
5.18e-18 |
SMART |
|
CA
|
141 |
224 |
5.68e-24 |
SMART |
|
CA
|
256 |
343 |
1.84e-23 |
SMART |
|
CA
|
367 |
449 |
2.99e-32 |
SMART |
|
CA
|
473 |
552 |
9.36e-25 |
SMART |
|
CA
|
578 |
659 |
9.9e-15 |
SMART |
|
transmembrane domain
|
691 |
713 |
N/A |
INTRINSIC |
|
low complexity region
|
737 |
764 |
N/A |
INTRINSIC |
|
low complexity region
|
812 |
825 |
N/A |
INTRINSIC |
|
low complexity region
|
903 |
914 |
N/A |
INTRINSIC |
|
low complexity region
|
1029 |
1040 |
N/A |
INTRINSIC |
|
low complexity region
|
1059 |
1071 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000193828
|
| SMART Domains |
Protein: ENSMUSP00000142328
Gene: ENSMUSG00000051375
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
18 |
48 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000194312
|
| Meta Mutation Damage Score |
0.0664 |
| Coding Region Coverage |
- 1x: 97.4%
- 3x: 96.9%
- 10x: 95.6%
- 20x: 93.5%
|
| Validation Efficiency |
100% (59/59) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the protocadherin subfamily within the cadherin superfamily. The encoded protein is a membrane protein found at cell-cell boundaries. It is involved in neural cell adhesion, suggesting a possible role in neuronal development. The protein includes an extracelllular region, containing 7 cadherin-like domains, a transmembrane region and a C-terminal cytoplasmic region. Cells expressing the protein showed cell aggregation activity. Alternative splicing occurs in this gene. [provided by RefSeq, Jul 2008]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc2 |
T |
C |
19: 43,786,945 (GRCm39) |
S189P |
probably benign |
Het |
| Adgrg3 |
G |
T |
8: 95,766,943 (GRCm39) |
V433F |
probably benign |
Het |
| Arhgap33 |
A |
T |
7: 30,222,234 (GRCm39) |
W1233R |
probably damaging |
Het |
| Brf2 |
T |
C |
8: 27,618,577 (GRCm39) |
D9G |
probably damaging |
Het |
| Btrc |
G |
A |
19: 45,515,839 (GRCm39) |
R562Q |
probably damaging |
Het |
| Cenpu |
T |
C |
8: 47,009,225 (GRCm39) |
F67L |
probably damaging |
Het |
| Chia1 |
T |
C |
3: 106,035,790 (GRCm39) |
M150T |
probably damaging |
Het |
| Cntln |
A |
G |
4: 85,019,072 (GRCm39) |
E1254G |
probably damaging |
Het |
| Creld1 |
G |
A |
6: 113,469,166 (GRCm39) |
C332Y |
probably damaging |
Het |
| Ctla2a |
A |
G |
13: 61,083,355 (GRCm39) |
|
probably benign |
Het |
| Dusp13b |
A |
T |
14: 21,785,043 (GRCm39) |
D223E |
probably benign |
Het |
| Ext1 |
C |
A |
15: 52,939,188 (GRCm39) |
L620F |
probably damaging |
Het |
| H2-DMb2 |
C |
T |
17: 34,366,834 (GRCm39) |
R89C |
probably damaging |
Het |
| Klhl32 |
A |
T |
4: 24,743,916 (GRCm39) |
L17* |
probably null |
Het |
| Lats2 |
C |
T |
14: 57,934,811 (GRCm39) |
V640M |
probably damaging |
Het |
| Lrig3 |
G |
A |
10: 125,845,694 (GRCm39) |
V708I |
possibly damaging |
Het |
| Mtcl1 |
T |
C |
17: 66,686,315 (GRCm39) |
T415A |
probably benign |
Het |
| Mynn |
A |
G |
3: 30,670,962 (GRCm39) |
*611W |
probably null |
Het |
| Nfx1 |
A |
G |
4: 41,009,240 (GRCm39) |
T793A |
possibly damaging |
Het |
| Nlrp4d |
T |
C |
7: 10,116,604 (GRCm39) |
|
noncoding transcript |
Het |
| Nos3 |
T |
C |
5: 24,573,818 (GRCm39) |
V194A |
probably damaging |
Het |
| Npc1l1 |
C |
T |
11: 6,167,473 (GRCm39) |
|
probably null |
Het |
| Nrg2 |
T |
C |
18: 36,154,150 (GRCm39) |
D589G |
probably damaging |
Het |
| Omg |
C |
T |
11: 79,392,545 (GRCm39) |
|
probably benign |
Het |
| Or10v9 |
T |
C |
19: 11,832,835 (GRCm39) |
T161A |
probably damaging |
Het |
| Or14j5 |
T |
C |
17: 38,161,839 (GRCm39) |
S119P |
probably damaging |
Het |
| Or2y17 |
A |
G |
11: 49,231,539 (GRCm39) |
Y60C |
probably damaging |
Het |
| Or8k16 |
T |
A |
2: 85,519,950 (GRCm39) |
M59K |
probably damaging |
Het |
| P2ry2 |
G |
T |
7: 100,648,058 (GRCm39) |
Y82* |
probably null |
Het |
| Pecr |
A |
T |
1: 72,314,136 (GRCm39) |
|
probably null |
Het |
| Pgm3 |
A |
G |
9: 86,447,743 (GRCm39) |
Y167H |
possibly damaging |
Het |
| Pramel15 |
A |
T |
4: 144,103,485 (GRCm39) |
C214S |
probably benign |
Het |
| Prmt2 |
T |
C |
10: 76,058,302 (GRCm39) |
H169R |
probably benign |
Het |
| Rad51ap2 |
T |
A |
12: 11,506,251 (GRCm39) |
S58T |
possibly damaging |
Het |
| Rbpms2 |
ACTGCTGCTGCTGCTGC |
ACTGCTGCTGCTGCTGCTGC |
9: 65,558,948 (GRCm39) |
|
probably benign |
Het |
| Slc6a15 |
T |
C |
10: 103,230,925 (GRCm39) |
S217P |
probably benign |
Het |
| Slco1a8 |
C |
A |
6: 141,939,363 (GRCm39) |
|
probably null |
Het |
| Snx27 |
G |
A |
3: 94,426,416 (GRCm39) |
T361I |
probably damaging |
Het |
| St7l |
A |
G |
3: 104,775,363 (GRCm39) |
T80A |
probably damaging |
Het |
| Stk32b |
T |
A |
5: 37,689,031 (GRCm39) |
M98L |
possibly damaging |
Het |
| Tonsl |
C |
A |
15: 76,508,350 (GRCm39) |
A6S |
possibly damaging |
Het |
| Tpx2 |
A |
G |
2: 152,711,611 (GRCm39) |
R49G |
probably benign |
Het |
| Trmt2a |
A |
G |
16: 18,067,758 (GRCm39) |
K144E |
possibly damaging |
Het |
| Trpm7 |
A |
C |
2: 126,654,697 (GRCm39) |
L1414V |
probably benign |
Het |
| Ugdh |
T |
C |
5: 65,580,939 (GRCm39) |
K107E |
possibly damaging |
Het |
| Vamp3 |
A |
T |
4: 151,135,366 (GRCm39) |
|
probably benign |
Het |
| Vmn1r172 |
T |
C |
7: 23,359,651 (GRCm39) |
S179P |
probably damaging |
Het |
| Vmn1r28 |
A |
G |
6: 58,242,963 (GRCm39) |
M269V |
probably benign |
Het |
| Vmn2r94 |
T |
C |
17: 18,464,476 (GRCm39) |
T605A |
probably benign |
Het |
| Vwce |
A |
G |
19: 10,615,520 (GRCm39) |
T134A |
possibly damaging |
Het |
| Zfp277 |
T |
C |
12: 40,495,745 (GRCm39) |
E5G |
probably benign |
Het |
|
| Other mutations in Pcdh1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00714:Pcdh1
|
APN |
18 |
38,331,782 (GRCm39) |
missense |
possibly damaging |
0.65 |
|
IGL00919:Pcdh1
|
APN |
18 |
38,335,865 (GRCm39) |
nonsense |
probably null |
|
|
IGL01744:Pcdh1
|
APN |
18 |
38,336,302 (GRCm39) |
missense |
probably damaging |
1.00 |
|
PIT4260001:Pcdh1
|
UTSW |
18 |
38,336,419 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0542:Pcdh1
|
UTSW |
18 |
38,322,975 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1449:Pcdh1
|
UTSW |
18 |
38,322,929 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1540:Pcdh1
|
UTSW |
18 |
38,322,779 (GRCm39) |
missense |
probably benign |
0.01 |
|
R1642:Pcdh1
|
UTSW |
18 |
38,332,283 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
R1672:Pcdh1
|
UTSW |
18 |
38,325,233 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1695:Pcdh1
|
UTSW |
18 |
38,335,921 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1727:Pcdh1
|
UTSW |
18 |
38,336,085 (GRCm39) |
nonsense |
probably null |
|
|
R1781:Pcdh1
|
UTSW |
18 |
38,322,977 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1793:Pcdh1
|
UTSW |
18 |
38,331,938 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1839:Pcdh1
|
UTSW |
18 |
38,332,538 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R1843:Pcdh1
|
UTSW |
18 |
38,325,278 (GRCm39) |
splice site |
probably null |
|
|
R2261:Pcdh1
|
UTSW |
18 |
38,331,710 (GRCm39) |
missense |
probably benign |
0.01 |
|
R2262:Pcdh1
|
UTSW |
18 |
38,331,710 (GRCm39) |
missense |
probably benign |
0.01 |
|
R2263:Pcdh1
|
UTSW |
18 |
38,331,710 (GRCm39) |
missense |
probably benign |
0.01 |
|
R2511:Pcdh1
|
UTSW |
18 |
38,332,532 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R2937:Pcdh1
|
UTSW |
18 |
38,322,815 (GRCm39) |
missense |
probably benign |
0.40 |
|
R3941:Pcdh1
|
UTSW |
18 |
38,332,511 (GRCm39) |
missense |
probably benign |
0.02 |
|
R3942:Pcdh1
|
UTSW |
18 |
38,332,511 (GRCm39) |
missense |
probably benign |
0.02 |
|
R4057:Pcdh1
|
UTSW |
18 |
38,331,950 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4155:Pcdh1
|
UTSW |
18 |
38,336,159 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4169:Pcdh1
|
UTSW |
18 |
38,331,358 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4617:Pcdh1
|
UTSW |
18 |
38,330,913 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4690:Pcdh1
|
UTSW |
18 |
38,336,528 (GRCm39) |
missense |
probably benign |
0.33 |
|
R4825:Pcdh1
|
UTSW |
18 |
38,322,912 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R5201:Pcdh1
|
UTSW |
18 |
38,331,971 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5266:Pcdh1
|
UTSW |
18 |
38,325,252 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5267:Pcdh1
|
UTSW |
18 |
38,325,252 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5351:Pcdh1
|
UTSW |
18 |
38,330,819 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5568:Pcdh1
|
UTSW |
18 |
38,330,420 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5729:Pcdh1
|
UTSW |
18 |
38,335,999 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5731:Pcdh1
|
UTSW |
18 |
38,331,651 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6043:Pcdh1
|
UTSW |
18 |
38,336,327 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R6278:Pcdh1
|
UTSW |
18 |
38,332,263 (GRCm39) |
missense |
probably benign |
0.29 |
|
R6333:Pcdh1
|
UTSW |
18 |
38,331,860 (GRCm39) |
missense |
probably benign |
0.25 |
|
R6498:Pcdh1
|
UTSW |
18 |
38,330,490 (GRCm39) |
missense |
probably benign |
0.18 |
|
R6937:Pcdh1
|
UTSW |
18 |
38,336,528 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R6994:Pcdh1
|
UTSW |
18 |
38,331,553 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7242:Pcdh1
|
UTSW |
18 |
38,336,270 (GRCm39) |
missense |
probably benign |
0.06 |
|
R7289:Pcdh1
|
UTSW |
18 |
38,322,966 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7391:Pcdh1
|
UTSW |
18 |
38,335,838 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R7702:Pcdh1
|
UTSW |
18 |
38,336,569 (GRCm39) |
missense |
unknown |
|
|
R7738:Pcdh1
|
UTSW |
18 |
38,330,529 (GRCm39) |
missense |
probably benign |
0.02 |
|
R7849:Pcdh1
|
UTSW |
18 |
38,322,662 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7941:Pcdh1
|
UTSW |
18 |
38,332,133 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8109:Pcdh1
|
UTSW |
18 |
38,332,049 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8675:Pcdh1
|
UTSW |
18 |
38,332,229 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8851:Pcdh1
|
UTSW |
18 |
38,325,155 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8947:Pcdh1
|
UTSW |
18 |
38,332,073 (GRCm39) |
missense |
possibly damaging |
0.89 |
|
R9443:Pcdh1
|
UTSW |
18 |
38,330,633 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9448:Pcdh1
|
UTSW |
18 |
38,330,492 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9608:Pcdh1
|
UTSW |
18 |
38,330,904 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
X0027:Pcdh1
|
UTSW |
18 |
38,322,841 (GRCm39) |
nonsense |
probably null |
|
|
Z1088:Pcdh1
|
UTSW |
18 |
38,331,120 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1176:Pcdh1
|
UTSW |
18 |
38,331,741 (GRCm39) |
missense |
possibly damaging |
0.79 |
|
| Predicted Primers |
PCR Primer
(F):5'- ATGGATCGGCAAACACTACAGC -3'
(R):5'- TGAGGCCCAGGAGCTATTTG -3'
Sequencing Primer
(F):5'- GAAGGAACCTTACACCTGCTTTTGG -3'
(R):5'- CCCAGGAGCTATTTGGACTACAG -3'
|
| Posted On |
2014-06-30 |
Incidental Mutation