Incidental Mutation 'R7939:Pcdha3'
| ID |
648969 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha3
|
| Ensembl Gene |
ENSMUSG00000102312 |
| Gene Name |
protocadherin alpha 3 |
| Synonyms |
|
| MMRRC Submission |
045985-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.116)
|
| Stock # |
R7939 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
18 |
| Chromosomal Location |
37079158-37320710 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 37080933 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Lysine
at position 558
(N558K)
|
| 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 damaging
Transcript: ENSMUST00000192503
AA Change: N558K
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000141989
Gene: ENSMUSG00000102312
AA Change: N558K
| 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 |
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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.0%
|
| 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: 67 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc12 |
A |
G |
8: 87,275,433 (GRCm39) |
I415T |
probably damaging |
Het |
| Ackr3 |
A |
G |
1: 90,142,287 (GRCm39) |
S249G |
probably benign |
Het |
| Adgre1 |
G |
T |
17: 57,756,938 (GRCm39) |
A732S |
probably damaging |
Het |
| Ahnak |
T |
A |
19: 8,991,448 (GRCm39) |
L4244* |
probably null |
Het |
| Aldh3a2 |
C |
A |
11: 61,115,424 (GRCm39) |
C511F |
probably benign |
Het |
| Ampd2 |
C |
A |
3: 107,987,432 (GRCm39) |
V134L |
probably benign |
Het |
| Ankrd11 |
A |
T |
8: 123,617,812 (GRCm39) |
H2013Q |
probably damaging |
Het |
| Atp5mc3 |
A |
G |
2: 73,740,206 (GRCm39) |
|
probably null |
Het |
| Calcoco2 |
GGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCC |
GGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTCCTCCCAGGAGGCCTTCTCTTTCTCCCAGGAGGCCTTCTCTTCC |
11: 95,990,808 (GRCm39) |
|
probably benign |
Het |
| Chtf18 |
A |
T |
17: 25,941,111 (GRCm39) |
I629N |
probably damaging |
Het |
| Clstn3 |
T |
C |
6: 124,439,158 (GRCm39) |
Y33C |
probably damaging |
Het |
| Cmc2 |
T |
C |
8: 117,616,513 (GRCm39) |
R71G |
unknown |
Het |
| Cts7 |
A |
T |
13: 61,504,364 (GRCm39) |
N66K |
probably damaging |
Het |
| Cysltr2 |
C |
T |
14: 73,267,399 (GRCm39) |
V104I |
possibly damaging |
Het |
| Dnai4 |
G |
A |
4: 102,953,798 (GRCm39) |
Q134* |
probably null |
Het |
| Dnm3 |
C |
T |
1: 162,123,165 (GRCm39) |
V460I |
possibly damaging |
Het |
| Ecel1 |
C |
T |
1: 87,077,256 (GRCm39) |
V651I |
probably benign |
Het |
| Ext2 |
G |
A |
2: 93,560,601 (GRCm39) |
R522C |
probably damaging |
Het |
| Farp2 |
T |
C |
1: 93,487,983 (GRCm39) |
L70P |
probably damaging |
Het |
| Fnip1 |
T |
C |
11: 54,393,093 (GRCm39) |
Y510H |
probably damaging |
Het |
| Gm15446 |
T |
C |
5: 110,090,360 (GRCm39) |
V204A |
probably benign |
Het |
| Gm29394 |
T |
C |
15: 57,912,046 (GRCm39) |
K53E |
unknown |
Het |
| Gm39115 |
T |
C |
7: 141,689,768 (GRCm39) |
T2A |
unknown |
Het |
| Helz2 |
A |
G |
2: 180,879,543 (GRCm39) |
W692R |
probably damaging |
Het |
| Htra2 |
A |
T |
6: 83,028,545 (GRCm39) |
Y428N |
probably damaging |
Het |
| Khdrbs2 |
T |
A |
1: 32,212,056 (GRCm39) |
S20T |
probably benign |
Het |
| Kifap3 |
C |
A |
1: 163,643,427 (GRCm39) |
Y217* |
probably null |
Het |
| Mast2 |
A |
T |
4: 116,287,668 (GRCm39) |
S136T |
probably benign |
Het |
| Mesp1 |
C |
T |
7: 79,442,734 (GRCm39) |
W181* |
probably null |
Het |
| Mtch1 |
A |
C |
17: 29,559,806 (GRCm39) |
S158A |
probably damaging |
Het |
| Mtmr10 |
C |
A |
7: 63,963,899 (GRCm39) |
S211R |
probably benign |
Het |
| Mtmr9 |
C |
A |
14: 63,771,973 (GRCm39) |
Q204H |
probably damaging |
Het |
| Myo5a |
A |
G |
9: 75,097,182 (GRCm39) |
N43D |
|
Het |
| Myom3 |
G |
T |
4: 135,534,589 (GRCm39) |
|
probably null |
Het |
| Neb |
T |
C |
2: 52,076,073 (GRCm39) |
D5903G |
probably damaging |
Het |
| Niban1 |
T |
G |
1: 151,581,775 (GRCm39) |
L457R |
probably damaging |
Het |
| Noxred1 |
A |
G |
12: 87,268,105 (GRCm39) |
V342A |
probably benign |
Het |
| Nsd2 |
T |
A |
5: 34,012,933 (GRCm39) |
S421R |
probably benign |
Het |
| Or10a3 |
T |
C |
7: 108,480,481 (GRCm39) |
I111V |
probably benign |
Het |
| Or5p55 |
T |
A |
7: 107,566,986 (GRCm39) |
C127* |
probably null |
Het |
| Oxa1l |
T |
C |
14: 54,604,876 (GRCm39) |
C270R |
probably benign |
Het |
| Pcdha7 |
T |
C |
18: 37,109,063 (GRCm39) |
V696A |
possibly damaging |
Het |
| Pigl |
T |
C |
11: 62,349,506 (GRCm39) |
L74P |
probably damaging |
Het |
| Plch2 |
G |
T |
4: 155,087,235 (GRCm39) |
R339S |
possibly damaging |
Het |
| Prdm11 |
G |
T |
2: 92,843,074 (GRCm39) |
D128E |
probably damaging |
Het |
| Ptdss1 |
A |
G |
13: 67,143,411 (GRCm39) |
T415A |
probably benign |
Het |
| Ptprj |
A |
T |
2: 90,295,009 (GRCm39) |
W400R |
probably damaging |
Het |
| Qdpr |
T |
C |
5: 45,607,407 (GRCm39) |
Y13C |
probably damaging |
Het |
| Retsat |
G |
A |
6: 72,581,919 (GRCm39) |
M355I |
probably benign |
Het |
| Slc24a1 |
T |
G |
9: 64,835,648 (GRCm39) |
E826D |
probably benign |
Het |
| Taok3 |
T |
C |
5: 117,331,902 (GRCm39) |
F40L |
probably benign |
Het |
| Tecta |
T |
C |
9: 42,299,519 (GRCm39) |
T190A |
probably damaging |
Het |
| Tmem220 |
C |
A |
11: 66,920,850 (GRCm39) |
T85K |
probably damaging |
Het |
| Traip |
T |
C |
9: 107,833,077 (GRCm39) |
F38L |
probably benign |
Het |
| Tspan1 |
A |
T |
4: 116,024,209 (GRCm39) |
I18N |
probably damaging |
Het |
| Ttc24 |
A |
T |
3: 87,981,945 (GRCm39) |
D40E |
possibly damaging |
Het |
| Ttn |
A |
T |
2: 76,542,737 (GRCm39) |
Y33416* |
probably null |
Het |
| Ttn |
A |
T |
2: 76,576,105 (GRCm39) |
D24929E |
probably damaging |
Het |
| Vmn2r16 |
T |
A |
5: 109,487,705 (GRCm39) |
S193T |
possibly damaging |
Het |
| Vmn2r83 |
T |
A |
10: 79,314,651 (GRCm39) |
W300R |
probably damaging |
Het |
| Vps13a |
C |
T |
19: 16,718,155 (GRCm39) |
V522M |
possibly damaging |
Het |
| Wdr17 |
C |
A |
8: 55,140,677 (GRCm39) |
R232L |
probably damaging |
Het |
| Wtap |
A |
T |
17: 13,200,683 (GRCm39) |
Y33* |
probably null |
Het |
| Zc3h10 |
A |
T |
10: 128,380,376 (GRCm39) |
V327E |
probably damaging |
Het |
| Zfp658 |
T |
C |
7: 43,224,301 (GRCm39) |
S859P |
possibly damaging |
Het |
| Zfp874b |
A |
T |
13: 67,622,622 (GRCm39) |
C225* |
probably null |
Het |
| Zfp980 |
A |
T |
4: 145,428,582 (GRCm39) |
H437L |
probably damaging |
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 |
|
R4090:Pcdha3
|
UTSW |
18 |
37,081,504 (GRCm39) |
missense |
probably benign |
0.04 |
|
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 |
|
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'- CTTGCTGTCGAGCTATGTGTCC -3'
(R):5'- TTCATCCAGGACACGTGTG -3'
Sequencing Primer
(F):5'- AGCTATGTGTCCGTGCAC -3'
(R):5'- TGATCTCACCGGTGTACAGAC -3'
|
| Posted On |
2020-09-15 |
Incidental Mutation