Incidental Mutation 'R5540:Pcdha4'
| ID |
435930 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha4
|
| Ensembl Gene |
ENSMUSG00000104252 |
| Gene Name |
protocadherin alpha 4 |
| Synonyms |
Crnr1, Cnr1 |
| MMRRC Submission |
043098-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.161)
|
| Stock # |
R5540 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
18 |
| Chromosomal Location |
37085742-37320710 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 37087890 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Alanine to Glutamic Acid
at position 691
(A691E)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000141408
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000070797]
[ENSMUST00000115661]
[ENSMUST00000115662]
[ENSMUST00000192295]
[ENSMUST00000192503]
[ENSMUST00000192512]
[ENSMUST00000193839]
[ENSMUST00000195590]
|
| AlphaFold |
no structure available at present |
| 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
AA Change: A691E
PolyPhen 2
Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458
AA Change: A691E
| 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
|
| SMART Domains |
Protein: ENSMUSP00000141989
Gene: ENSMUSG00000102312
| 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
AA Change: A691E
PolyPhen 2
Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000141408
Gene: ENSMUSG00000104252
AA Change: A691E
| 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 |
noncoding transcript
Transcript: ENSMUST00000194235
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000194001
|
| 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: 99.9%
- 3x: 99.7%
- 10x: 98.6%
- 20x: 96.1%
|
| 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: 74 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700008O03Rik |
A |
G |
7: 44,012,371 (GRCm39) |
S15P |
probably damaging |
Het |
| Actl7a |
A |
T |
4: 56,744,388 (GRCm39) |
H305L |
probably benign |
Het |
| Adam26b |
C |
A |
8: 43,974,654 (GRCm39) |
C116F |
probably damaging |
Het |
| Adgrl2 |
A |
G |
3: 148,543,198 (GRCm39) |
|
probably null |
Het |
| Akr1b10 |
A |
G |
6: 34,371,047 (GRCm39) |
T238A |
probably damaging |
Het |
| Akr1c18 |
A |
G |
13: 4,187,178 (GRCm39) |
V186A |
probably benign |
Het |
| Alpk3 |
G |
A |
7: 80,745,184 (GRCm39) |
V1311M |
probably damaging |
Het |
| Aox1 |
A |
G |
1: 58,143,569 (GRCm39) |
N1229S |
probably benign |
Het |
| Apobec3 |
T |
A |
15: 79,782,120 (GRCm39) |
N43K |
probably benign |
Het |
| Arid1a |
A |
C |
4: 133,407,765 (GRCm39) |
D2247E |
unknown |
Het |
| Asph |
A |
G |
4: 9,635,906 (GRCm39) |
L77S |
probably damaging |
Het |
| Cd300ld |
T |
A |
11: 114,878,231 (GRCm39) |
T94S |
probably damaging |
Het |
| Celf2 |
T |
C |
2: 6,558,743 (GRCm39) |
T382A |
probably benign |
Het |
| Cfap54 |
C |
T |
10: 92,808,470 (GRCm39) |
A1402T |
possibly damaging |
Het |
| Chrnb1 |
A |
T |
11: 69,686,476 (GRCm39) |
V48E |
probably benign |
Het |
| Col6a5 |
T |
A |
9: 105,739,975 (GRCm39) |
E2548V |
probably benign |
Het |
| Crebrf |
A |
G |
17: 26,961,071 (GRCm39) |
D56G |
possibly damaging |
Het |
| Dctn5 |
A |
G |
7: 121,734,275 (GRCm39) |
T40A |
probably benign |
Het |
| Dmxl2 |
A |
T |
9: 54,301,141 (GRCm39) |
N2323K |
probably benign |
Het |
| Dync1h1 |
A |
G |
12: 110,627,384 (GRCm39) |
Q4021R |
probably benign |
Het |
| Dyrk1a |
T |
G |
16: 94,486,202 (GRCm39) |
|
probably null |
Het |
| Ephb3 |
T |
A |
16: 21,039,610 (GRCm39) |
F454Y |
probably damaging |
Het |
| Fbxo38 |
A |
G |
18: 62,647,864 (GRCm39) |
|
probably null |
Het |
| Flg |
T |
C |
3: 93,184,923 (GRCm39) |
F15S |
probably damaging |
Het |
| Fndc3b |
G |
A |
3: 27,555,651 (GRCm39) |
P301L |
probably damaging |
Het |
| Fpr-rs7 |
C |
T |
17: 20,334,356 (GRCm39) |
G45R |
probably damaging |
Het |
| Garin3 |
A |
G |
11: 46,295,715 (GRCm39) |
N29S |
probably damaging |
Het |
| Gfi1 |
T |
A |
5: 107,867,991 (GRCm39) |
T360S |
probably damaging |
Het |
| Grik4 |
T |
C |
9: 42,432,243 (GRCm39) |
H918R |
probably damaging |
Het |
| Hpx |
A |
G |
7: 105,241,119 (GRCm39) |
S385P |
possibly damaging |
Het |
| Kdm5b |
A |
G |
1: 134,558,979 (GRCm39) |
D1501G |
probably damaging |
Het |
| Kif20b |
A |
T |
19: 34,915,860 (GRCm39) |
M546L |
probably benign |
Het |
| Map3k9 |
G |
T |
12: 81,819,587 (GRCm39) |
N222K |
probably damaging |
Het |
| Me1 |
A |
G |
9: 86,561,926 (GRCm39) |
L53P |
possibly damaging |
Het |
| Mis18bp1 |
T |
C |
12: 65,195,520 (GRCm39) |
E748G |
possibly damaging |
Het |
| Morc3 |
T |
A |
16: 93,644,268 (GRCm39) |
N186K |
probably benign |
Het |
| Mtor |
A |
G |
4: 148,539,165 (GRCm39) |
T221A |
probably benign |
Het |
| Muc6 |
A |
G |
7: 141,235,850 (GRCm39) |
|
probably null |
Het |
| Myh8 |
C |
A |
11: 67,177,266 (GRCm39) |
T444N |
probably benign |
Het |
| Myo7b |
A |
G |
18: 32,140,143 (GRCm39) |
Y216H |
probably damaging |
Het |
| Myom1 |
G |
A |
17: 71,416,782 (GRCm39) |
V1382M |
probably damaging |
Het |
| Nbeal2 |
A |
T |
9: 110,460,801 (GRCm39) |
Y1718N |
probably damaging |
Het |
| Npc1l1 |
A |
G |
11: 6,164,546 (GRCm39) |
S1168P |
probably damaging |
Het |
| Or4c58 |
A |
G |
2: 89,675,011 (GRCm39) |
F102S |
probably damaging |
Het |
| Or4d2 |
T |
A |
11: 87,784,511 (GRCm39) |
K80* |
probably null |
Het |
| Or51f5 |
C |
T |
7: 102,424,136 (GRCm39) |
A135V |
probably benign |
Het |
| Or5an9 |
T |
A |
19: 12,187,824 (GRCm39) |
I298N |
probably damaging |
Het |
| Or6c8b |
G |
T |
10: 128,882,364 (GRCm39) |
D189E |
probably damaging |
Het |
| Pde6a |
T |
G |
18: 61,364,438 (GRCm39) |
F165V |
probably damaging |
Het |
| Ptpn14 |
A |
T |
1: 189,578,561 (GRCm39) |
M340L |
probably benign |
Het |
| Rnasel |
G |
T |
1: 153,630,890 (GRCm39) |
E469* |
probably null |
Het |
| Rsph3a |
T |
G |
17: 8,164,790 (GRCm39) |
L50R |
probably benign |
Het |
| Rusc2 |
A |
G |
4: 43,423,975 (GRCm39) |
Y1043C |
probably damaging |
Het |
| Serpinb6b |
A |
T |
13: 33,161,541 (GRCm39) |
K86* |
probably null |
Het |
| Serpine1 |
T |
C |
5: 137,092,063 (GRCm39) |
T392A |
probably benign |
Het |
| Shcbp1 |
A |
T |
8: 4,794,529 (GRCm39) |
D421E |
probably damaging |
Het |
| Slc24a1 |
A |
G |
9: 64,855,863 (GRCm39) |
V348A |
unknown |
Het |
| Slc26a7 |
A |
G |
4: 14,506,621 (GRCm39) |
F605L |
probably benign |
Het |
| Slc66a1 |
A |
T |
4: 139,027,655 (GRCm39) |
L229Q |
probably damaging |
Het |
| Spag17 |
A |
C |
3: 99,963,588 (GRCm39) |
E1102A |
possibly damaging |
Het |
| Stab2 |
A |
G |
10: 86,683,989 (GRCm39) |
V2390A |
probably benign |
Het |
| Stk11 |
A |
G |
10: 79,961,883 (GRCm39) |
I35V |
probably benign |
Het |
| Stk24 |
T |
C |
14: 121,531,693 (GRCm39) |
D321G |
possibly damaging |
Het |
| Tbx4 |
A |
T |
11: 85,801,994 (GRCm39) |
N209I |
possibly damaging |
Het |
| Tmem225 |
T |
C |
9: 40,060,681 (GRCm39) |
L80P |
probably damaging |
Het |
| Tnfrsf4 |
C |
T |
4: 156,098,380 (GRCm39) |
T17I |
probably benign |
Het |
| Traf3ip1 |
G |
A |
1: 91,429,037 (GRCm39) |
R268Q |
probably benign |
Het |
| Trhde |
T |
A |
10: 114,636,497 (GRCm39) |
I237F |
probably benign |
Het |
| Ugt2a1 |
A |
T |
5: 87,633,915 (GRCm39) |
W231R |
probably damaging |
Het |
| Vash1 |
ACTGCTGCTGCTGCTGCTGC |
ACTGCTGCTGCTGCTGC |
12: 86,726,831 (GRCm39) |
|
probably benign |
Het |
| Vps16 |
T |
A |
2: 130,284,305 (GRCm39) |
D685E |
probably benign |
Het |
| Washc4 |
A |
G |
10: 83,409,657 (GRCm39) |
D602G |
probably damaging |
Het |
| Wdr59 |
A |
G |
8: 112,211,816 (GRCm39) |
L377P |
possibly damaging |
Het |
| Wdr81 |
T |
C |
11: 75,339,896 (GRCm39) |
E1364G |
probably damaging |
Het |
|
| Other mutations in Pcdha4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
R2570:Pcdha4
|
UTSW |
18 |
37,086,665 (GRCm39) |
missense |
probably benign |
0.00 |
|
R3114:Pcdha4
|
UTSW |
18 |
37,086,603 (GRCm39) |
missense |
probably benign |
0.02 |
|
R3115:Pcdha4
|
UTSW |
18 |
37,086,603 (GRCm39) |
missense |
probably benign |
0.02 |
|
R4154:Pcdha4
|
UTSW |
18 |
37,086,639 (GRCm39) |
splice site |
probably null |
|
|
R4381:Pcdha4
|
UTSW |
18 |
37,085,928 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4389:Pcdha4
|
UTSW |
18 |
37,087,842 (GRCm39) |
missense |
probably benign |
|
|
R4493:Pcdha4
|
UTSW |
18 |
37,087,644 (GRCm39) |
missense |
possibly damaging |
0.80 |
|
R4801:Pcdha4
|
UTSW |
18 |
37,087,008 (GRCm39) |
nonsense |
probably null |
|
|
R4802:Pcdha4
|
UTSW |
18 |
37,087,008 (GRCm39) |
nonsense |
probably null |
|
|
R4827:Pcdha4
|
UTSW |
18 |
37,086,251 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4928:Pcdha4
|
UTSW |
18 |
37,087,869 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5001:Pcdha4
|
UTSW |
18 |
37,088,001 (GRCm39) |
missense |
probably benign |
|
|
R5330:Pcdha4
|
UTSW |
18 |
37,087,755 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5331:Pcdha4
|
UTSW |
18 |
37,087,755 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5587:Pcdha4
|
UTSW |
18 |
37,087,875 (GRCm39) |
missense |
probably benign |
|
|
R5931:Pcdha4
|
UTSW |
18 |
37,087,808 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6249:Pcdha4
|
UTSW |
18 |
37,086,729 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6427:Pcdha4
|
UTSW |
18 |
37,086,786 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6612:Pcdha4
|
UTSW |
18 |
37,088,031 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6616:Pcdha4
|
UTSW |
18 |
37,086,953 (GRCm39) |
missense |
probably benign |
|
|
R7030:Pcdha4
|
UTSW |
18 |
37,087,080 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7198:Pcdha4
|
UTSW |
18 |
37,086,613 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7411:Pcdha4
|
UTSW |
18 |
37,086,111 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7491:Pcdha4
|
UTSW |
18 |
37,087,689 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7513:Pcdha4
|
UTSW |
18 |
37,086,392 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7544:Pcdha4
|
UTSW |
18 |
37,086,776 (GRCm39) |
missense |
probably benign |
0.05 |
|
R7735:Pcdha4
|
UTSW |
18 |
37,085,961 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7753:Pcdha4
|
UTSW |
18 |
37,086,354 (GRCm39) |
missense |
possibly damaging |
0.49 |
|
R8104:Pcdha4
|
UTSW |
18 |
37,087,106 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8239:Pcdha4
|
UTSW |
18 |
37,086,128 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8767:Pcdha4
|
UTSW |
18 |
37,086,905 (GRCm39) |
missense |
possibly damaging |
0.73 |
|
R8802:Pcdha4
|
UTSW |
18 |
37,087,211 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R8869:Pcdha4
|
UTSW |
18 |
37,086,011 (GRCm39) |
nonsense |
probably null |
|
|
R9102:Pcdha4
|
UTSW |
18 |
37,087,630 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9365:Pcdha4
|
UTSW |
18 |
37,087,112 (GRCm39) |
missense |
possibly damaging |
0.92 |
|
R9593:Pcdha4
|
UTSW |
18 |
37,086,740 (GRCm39) |
missense |
probably benign |
0.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- AGAAGGCAATTCCCGTAGCC -3'
(R):5'- TTGGGAGTATGACCAGCTCC -3'
Sequencing Primer
(F):5'- CGAGATTAGTACTACGCGCATACTG -3'
(R):5'- GAGTATGACCAGCTCCCCACTG -3'
|
| Posted On |
2016-10-24 |
Incidental Mutation