Incidental Mutation 'R4090:Pcdha3'
ID |
317584 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Pcdha3
|
Ensembl Gene |
ENSMUSG00000102312 |
Gene Name |
protocadherin alpha 3 |
Synonyms |
|
MMRRC Submission |
040983-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.111)
|
Stock # |
R4090 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
18 |
Chromosomal Location |
37079158-37320710 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 37081504 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Arginine to Glycine
at position 749
(R749G)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000141989
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000070797]
[ENSMUST00000115661]
[ENSMUST00000115662]
[ENSMUST00000192295]
[ENSMUST00000192503]
[ENSMUST00000192512]
[ENSMUST00000193839]
[ENSMUST00000195590]
|
AlphaFold |
Q91Y16 |
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 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: 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
AA Change: R749G
PolyPhen 2
Score 0.040 (Sensitivity: 0.94; Specificity: 0.83)
|
SMART Domains |
Protein: ENSMUSP00000141989 Gene: ENSMUSG00000102312 AA Change: R749G
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 |
noncoding transcript
Transcript: ENSMUST00000194001
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000194235
|
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 |
|
Meta Mutation Damage Score |
0.3701 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.7%
|
Validation Efficiency |
96% (53/55) |
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: 48 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Acss3 |
T |
G |
10: 106,889,313 (GRCm39) |
Y169S |
probably damaging |
Het |
Apc2 |
A |
G |
10: 80,141,378 (GRCm39) |
K268E |
probably damaging |
Het |
Arhgef2 |
G |
C |
3: 88,551,185 (GRCm39) |
R765P |
probably benign |
Het |
Bptf |
T |
C |
11: 106,972,349 (GRCm39) |
K840E |
probably damaging |
Het |
Carf |
A |
G |
1: 60,175,506 (GRCm39) |
R245G |
possibly damaging |
Het |
Cd36 |
A |
G |
5: 17,990,718 (GRCm39) |
|
probably null |
Het |
Cep250 |
G |
A |
2: 155,834,552 (GRCm39) |
R2159K |
probably damaging |
Het |
Cldn34c4 |
A |
T |
X: 126,629,011 (GRCm39) |
V153E |
probably damaging |
Het |
Col4a4 |
T |
A |
1: 82,501,643 (GRCm39) |
Y370F |
unknown |
Het |
Cplane1 |
T |
A |
15: 8,241,842 (GRCm39) |
|
probably null |
Het |
Ddx4 |
A |
G |
13: 112,750,295 (GRCm39) |
V386A |
probably benign |
Het |
Exoc6 |
A |
G |
19: 37,560,360 (GRCm39) |
T126A |
probably benign |
Het |
Fam83f |
A |
T |
15: 80,576,393 (GRCm39) |
N348I |
possibly damaging |
Het |
Gja8 |
A |
G |
3: 96,826,468 (GRCm39) |
V398A |
probably benign |
Het |
Gkn3 |
C |
T |
6: 87,360,507 (GRCm39) |
A163T |
probably damaging |
Het |
Gm12789 |
A |
T |
4: 101,845,526 (GRCm39) |
T72S |
possibly damaging |
Het |
Gm1988 |
A |
G |
7: 38,820,292 (GRCm39) |
|
noncoding transcript |
Het |
Gm21370 |
A |
G |
13: 120,488,489 (GRCm39) |
V20A |
probably benign |
Het |
Hjurp |
G |
C |
1: 88,204,937 (GRCm39) |
|
probably benign |
Het |
Hsd17b13 |
T |
A |
5: 104,113,720 (GRCm39) |
S245C |
probably benign |
Het |
Htr1f |
T |
C |
16: 64,746,324 (GRCm39) |
K323E |
probably benign |
Het |
Igkc |
T |
C |
6: 70,703,442 (GRCm39) |
|
probably benign |
Het |
Ksr1 |
T |
C |
11: 78,918,303 (GRCm39) |
E535G |
probably damaging |
Het |
Mlxipl |
A |
T |
5: 135,161,381 (GRCm39) |
E433D |
probably benign |
Het |
Npc1 |
T |
C |
18: 12,331,219 (GRCm39) |
|
probably null |
Het |
Or10ak7 |
C |
T |
4: 118,791,230 (GRCm39) |
E272K |
probably benign |
Het |
Or1e29 |
A |
G |
11: 73,667,667 (GRCm39) |
L162P |
probably damaging |
Het |
Or6y1 |
A |
G |
1: 174,276,500 (GRCm39) |
T104A |
probably benign |
Het |
Or7g17 |
T |
C |
9: 18,768,398 (GRCm39) |
I159T |
probably benign |
Het |
Ppme1 |
A |
T |
7: 99,997,044 (GRCm39) |
N122K |
possibly damaging |
Het |
Rasal1 |
G |
A |
5: 120,813,674 (GRCm39) |
V657M |
possibly damaging |
Het |
Rbm47 |
A |
G |
5: 66,180,080 (GRCm39) |
M409T |
probably benign |
Het |
Rragd |
C |
T |
4: 33,007,155 (GRCm39) |
T161M |
probably damaging |
Het |
Slurp1 |
T |
C |
15: 74,598,724 (GRCm39) |
H89R |
possibly damaging |
Het |
Snap23 |
A |
G |
2: 120,416,061 (GRCm39) |
I42V |
probably benign |
Het |
Sypl2 |
A |
G |
3: 108,124,992 (GRCm39) |
I123T |
possibly damaging |
Het |
Taar8a |
T |
A |
10: 23,953,062 (GRCm39) |
V222E |
probably damaging |
Het |
Tmem171 |
A |
T |
13: 98,829,096 (GRCm39) |
V18D |
probably damaging |
Het |
Topors |
T |
C |
4: 40,260,794 (GRCm39) |
D830G |
unknown |
Het |
Traf3ip3 |
A |
G |
1: 192,863,628 (GRCm39) |
V414A |
probably damaging |
Het |
Tubg1 |
T |
A |
11: 101,015,364 (GRCm39) |
M270K |
possibly damaging |
Het |
Vmn1r188 |
T |
C |
13: 22,272,772 (GRCm39) |
V242A |
probably benign |
Het |
Vmn1r19 |
T |
A |
6: 57,381,720 (GRCm39) |
I91N |
probably damaging |
Het |
Vmn2r12 |
T |
A |
5: 109,239,412 (GRCm39) |
M384L |
probably benign |
Het |
Wdr26 |
T |
C |
1: 181,030,679 (GRCm39) |
E205G |
probably damaging |
Het |
Zfp281 |
T |
A |
1: 136,553,859 (GRCm39) |
I279N |
probably damaging |
Het |
Zfp398 |
T |
A |
6: 47,843,159 (GRCm39) |
C272S |
probably damaging |
Het |
Zfp975 |
A |
G |
7: 42,312,298 (GRCm39) |
V105A |
probably benign |
Het |
|
Other mutations in Pcdha3 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
R2497:Pcdha3
|
UTSW |
18 |
37,080,556 (GRCm39) |
missense |
probably benign |
|
R3702:Pcdha3
|
UTSW |
18 |
37,080,401 (GRCm39) |
missense |
probably benign |
0.16 |
R4273:Pcdha3
|
UTSW |
18 |
37,081,144 (GRCm39) |
missense |
probably damaging |
1.00 |
R4486:Pcdha3
|
UTSW |
18 |
37,080,404 (GRCm39) |
missense |
probably damaging |
1.00 |
R4535:Pcdha3
|
UTSW |
18 |
37,081,013 (GRCm39) |
missense |
probably damaging |
1.00 |
R4582:Pcdha3
|
UTSW |
18 |
37,080,485 (GRCm39) |
missense |
probably benign |
|
R4712:Pcdha3
|
UTSW |
18 |
37,079,560 (GRCm39) |
missense |
probably damaging |
1.00 |
R5160:Pcdha3
|
UTSW |
18 |
37,079,480 (GRCm39) |
missense |
probably damaging |
1.00 |
R5302:Pcdha3
|
UTSW |
18 |
37,081,208 (GRCm39) |
missense |
probably damaging |
0.96 |
R5361:Pcdha3
|
UTSW |
18 |
37,079,752 (GRCm39) |
missense |
possibly damaging |
0.80 |
R5535:Pcdha3
|
UTSW |
18 |
37,080,989 (GRCm39) |
missense |
probably benign |
0.02 |
R5682:Pcdha3
|
UTSW |
18 |
37,081,040 (GRCm39) |
missense |
probably damaging |
0.99 |
R6656:Pcdha3
|
UTSW |
18 |
37,080,875 (GRCm39) |
missense |
probably benign |
0.24 |
R6878:Pcdha3
|
UTSW |
18 |
37,080,416 (GRCm39) |
nonsense |
probably null |
|
R7150:Pcdha3
|
UTSW |
18 |
37,080,165 (GRCm39) |
missense |
probably benign |
0.01 |
R7167:Pcdha3
|
UTSW |
18 |
37,080,046 (GRCm39) |
missense |
probably damaging |
1.00 |
R7299:Pcdha3
|
UTSW |
18 |
37,079,977 (GRCm39) |
missense |
possibly damaging |
0.56 |
R7301:Pcdha3
|
UTSW |
18 |
37,079,977 (GRCm39) |
missense |
possibly damaging |
0.56 |
R7448:Pcdha3
|
UTSW |
18 |
37,079,266 (GRCm39) |
missense |
probably benign |
0.00 |
R7467:Pcdha3
|
UTSW |
18 |
37,080,584 (GRCm39) |
missense |
probably damaging |
1.00 |
R7542:Pcdha3
|
UTSW |
18 |
37,080,784 (GRCm39) |
missense |
possibly damaging |
0.86 |
R7659:Pcdha3
|
UTSW |
18 |
37,081,219 (GRCm39) |
missense |
probably benign |
0.14 |
R7761:Pcdha3
|
UTSW |
18 |
37,079,347 (GRCm39) |
missense |
probably damaging |
1.00 |
R7782:Pcdha3
|
UTSW |
18 |
37,081,193 (GRCm39) |
missense |
probably damaging |
0.98 |
R7939:Pcdha3
|
UTSW |
18 |
37,080,933 (GRCm39) |
missense |
probably damaging |
1.00 |
R8217:Pcdha3
|
UTSW |
18 |
37,079,974 (GRCm39) |
missense |
probably damaging |
0.99 |
R8440:Pcdha3
|
UTSW |
18 |
37,080,914 (GRCm39) |
missense |
probably damaging |
1.00 |
R8938:Pcdha3
|
UTSW |
18 |
37,080,154 (GRCm39) |
missense |
probably benign |
0.43 |
R9375:Pcdha3
|
UTSW |
18 |
37,079,353 (GRCm39) |
missense |
probably benign |
0.29 |
R9378:Pcdha3
|
UTSW |
18 |
37,080,284 (GRCm39) |
missense |
probably damaging |
1.00 |
R9546:Pcdha3
|
UTSW |
18 |
37,079,389 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Predicted Primers |
PCR Primer
(F):5'- TACCTGATCATCGCCATCTGTG -3'
(R):5'- TAGCGAGTGTAAAGTTCTCTACAG -3'
Sequencing Primer
(F):5'- GCCATCTGTGCCGTGTCTAG -3'
(R):5'- GAATAGTTCATTTTAACGCCATCTCC -3'
|
Posted On |
2015-05-15 |