Incidental Mutation 'R3941:Pcdh1'
ID |
307480 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Pcdh1
|
Ensembl Gene |
ENSMUSG00000051375 |
Gene Name |
protocadherin 1 |
Synonyms |
2010005A06Rik |
MMRRC Submission |
040923-MU
|
Accession Numbers |
|
Essential gene? |
Possibly non essential
(E-score: 0.330)
|
Stock # |
R3941 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
18 |
Chromosomal Location |
38318967-38345023 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 38332511 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Alanine
at position 164
(V164A)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000125576
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000057185]
[ENSMUST00000159405]
[ENSMUST00000160721]
[ENSMUST00000161701]
[ENSMUST00000193828]
[ENSMUST00000194312]
|
AlphaFold |
Q8CFX3 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000057185
AA Change: V303A
PolyPhen 2
Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
|
SMART Domains |
Protein: ENSMUSP00000055199 Gene: ENSMUSG00000051375 AA Change: V303A
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: ENSMUST00000159405
AA Change: V303A
PolyPhen 2
Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
|
SMART Domains |
Protein: ENSMUSP00000125309 Gene: ENSMUSG00000051375 AA Change: V303A
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
|
SMART Domains |
Protein: ENSMUSP00000124732 Gene: ENSMUSG00000051375
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: V164A
PolyPhen 2
Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)
|
SMART Domains |
Protein: ENSMUSP00000125576 Gene: ENSMUSG00000051375 AA Change: V164A
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 |
0.0698 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.3%
|
Validation Efficiency |
98% (55/56) |
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: 52 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abcc1 |
A |
T |
16: 14,214,263 (GRCm39) |
T193S |
probably benign |
Het |
Arhgap11a |
A |
T |
2: 113,667,242 (GRCm39) |
L435Q |
probably damaging |
Het |
Bin1 |
T |
C |
18: 32,539,211 (GRCm39) |
V48A |
probably damaging |
Het |
Brinp3 |
C |
A |
1: 146,627,599 (GRCm39) |
D277E |
probably damaging |
Het |
Btn1a1 |
T |
G |
13: 23,643,434 (GRCm39) |
R338S |
probably benign |
Het |
Cacnb4 |
C |
A |
2: 52,359,501 (GRCm39) |
R169L |
probably damaging |
Het |
Ccdc80 |
A |
G |
16: 44,916,455 (GRCm39) |
T404A |
probably benign |
Het |
Cd2ap |
G |
C |
17: 43,119,690 (GRCm39) |
H488D |
probably damaging |
Het |
Cdon |
A |
G |
9: 35,375,467 (GRCm39) |
T498A |
probably benign |
Het |
Cngb3 |
A |
G |
4: 19,396,786 (GRCm39) |
N380D |
probably benign |
Het |
Col6a5 |
G |
A |
9: 105,817,033 (GRCm39) |
S426F |
unknown |
Het |
Cr2 |
A |
T |
1: 194,848,122 (GRCm39) |
H345Q |
probably damaging |
Het |
Cttnbp2 |
T |
A |
6: 18,427,452 (GRCm39) |
K743M |
probably benign |
Het |
Depdc1b |
T |
C |
13: 108,505,370 (GRCm39) |
S245P |
probably damaging |
Het |
Dync2h1 |
G |
A |
9: 7,124,825 (GRCm39) |
H2016Y |
probably benign |
Het |
Eif2s3y |
G |
T |
Y: 1,012,079 (GRCm39) |
R98L |
probably benign |
Het |
Eml6 |
C |
T |
11: 29,753,167 (GRCm39) |
G915S |
probably damaging |
Het |
Fcgr1 |
A |
G |
3: 96,193,349 (GRCm39) |
L216P |
probably benign |
Het |
Fpr-rs3 |
T |
C |
17: 20,845,111 (GRCm39) |
N10S |
probably benign |
Het |
Frem3 |
T |
C |
8: 81,341,649 (GRCm39) |
I1314T |
possibly damaging |
Het |
Gabrr3 |
A |
G |
16: 59,253,864 (GRCm39) |
N194D |
probably damaging |
Het |
Hey1 |
A |
G |
3: 8,729,638 (GRCm39) |
L273P |
probably damaging |
Het |
Irf6 |
A |
G |
1: 192,850,857 (GRCm39) |
K365E |
probably benign |
Het |
Kit |
A |
G |
5: 75,769,978 (GRCm39) |
D130G |
probably benign |
Het |
Lrp1 |
G |
A |
10: 127,389,265 (GRCm39) |
A3217V |
probably damaging |
Het |
Mei4 |
C |
T |
9: 81,809,336 (GRCm39) |
R140C |
probably benign |
Het |
Mir100hg |
T |
C |
9: 41,501,570 (GRCm39) |
L143P |
probably damaging |
Het |
Mpo |
A |
T |
11: 87,688,175 (GRCm39) |
K278M |
probably benign |
Het |
Mprip |
T |
C |
11: 59,622,328 (GRCm39) |
|
probably benign |
Het |
Mug2 |
G |
C |
6: 122,040,522 (GRCm39) |
G691R |
probably benign |
Het |
Neto2 |
G |
A |
8: 86,400,747 (GRCm39) |
T16I |
probably damaging |
Het |
Nipal4 |
C |
T |
11: 46,041,473 (GRCm39) |
V241M |
probably damaging |
Het |
Nlrp2 |
A |
T |
7: 5,330,551 (GRCm39) |
L615* |
probably null |
Het |
Phc2 |
T |
C |
4: 128,641,037 (GRCm39) |
|
probably null |
Het |
Plekhg3 |
A |
G |
12: 76,620,133 (GRCm39) |
E623G |
probably damaging |
Het |
Psors1c2 |
G |
T |
17: 35,844,825 (GRCm39) |
G29* |
probably null |
Het |
Slc25a54 |
A |
T |
3: 109,019,479 (GRCm39) |
D361V |
probably damaging |
Het |
Slc39a12 |
A |
T |
2: 14,400,992 (GRCm39) |
H123L |
possibly damaging |
Het |
Sorl1 |
T |
C |
9: 41,900,764 (GRCm39) |
|
probably null |
Het |
Strn |
A |
T |
17: 78,965,369 (GRCm39) |
I641N |
probably damaging |
Het |
Tapbp |
A |
G |
17: 34,139,457 (GRCm39) |
E151G |
possibly damaging |
Het |
Ticrr |
T |
C |
7: 79,343,445 (GRCm39) |
|
probably benign |
Het |
Tnfrsf21 |
G |
A |
17: 43,348,901 (GRCm39) |
C171Y |
probably damaging |
Het |
Ttyh1 |
T |
A |
7: 4,132,317 (GRCm39) |
L155H |
probably damaging |
Het |
Utrn |
T |
A |
10: 12,587,329 (GRCm39) |
|
probably null |
Het |
Vmn1r175 |
A |
G |
7: 23,508,393 (GRCm39) |
V78A |
probably benign |
Het |
Vmn1r73 |
T |
C |
7: 11,490,682 (GRCm39) |
Y167H |
probably damaging |
Het |
Washc1 |
T |
C |
17: 66,425,123 (GRCm39) |
S376P |
probably damaging |
Het |
Wnt10a |
T |
A |
1: 74,842,656 (GRCm39) |
|
probably null |
Het |
Xrcc4 |
A |
G |
13: 90,219,752 (GRCm39) |
V16A |
probably benign |
Het |
Zeb1 |
T |
C |
18: 5,767,799 (GRCm39) |
V770A |
probably benign |
Het |
Zfp410 |
A |
G |
12: 84,385,527 (GRCm39) |
N90S |
probably damaging |
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 |
|
R1882:Pcdh1
|
UTSW |
18 |
38,335,895 (GRCm39) |
missense |
possibly damaging |
0.49 |
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 |
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'- TGATGAGTCACCAGCCCTATG -3'
(R):5'- CCATGTGCCGCTTATGGAAAG -3'
Sequencing Primer
(F):5'- AGCCCTATGCCTCGGATC -3'
(R):5'- CCGCTTATGGAAAGGGTGC -3'
|
Posted On |
2015-04-17 |