Incidental Mutation 'R4273:Pcdha3'
| ID |
322309 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha3
|
| Ensembl Gene |
ENSMUSG00000102312 |
| Gene Name |
protocadherin alpha 3 |
| Synonyms |
|
| MMRRC Submission |
041645-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.111)
|
| Stock # |
R4273 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
18 |
| Chromosomal Location |
37079158-37320710 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 37081144 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Cysteine
at position 629
(R629C)
|
| 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: R629C
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000141989
Gene: ENSMUSG00000102312
AA Change: R629C
| 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 |
noncoding transcript
Transcript: ENSMUST00000194001
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000194235
|
| 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: 99.4%
- 3x: 98.8%
- 10x: 97.7%
- 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: 65 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acer2 |
T |
A |
4: 86,792,835 (GRCm39) |
|
probably null |
Het |
| Adgrf2 |
T |
A |
17: 43,021,013 (GRCm39) |
T604S |
probably damaging |
Het |
| Akap8l |
T |
A |
17: 32,540,905 (GRCm39) |
K533* |
probably null |
Het |
| Appbp2 |
T |
C |
11: 85,125,502 (GRCm39) |
Y45C |
probably damaging |
Het |
| Arap2 |
T |
C |
5: 62,828,322 (GRCm39) |
I950V |
possibly damaging |
Het |
| Arhgap31 |
T |
C |
16: 38,422,697 (GRCm39) |
E1123G |
possibly damaging |
Het |
| Atp2c1 |
G |
T |
9: 105,312,339 (GRCm39) |
N493K |
probably benign |
Het |
| Bcr |
T |
C |
10: 74,960,943 (GRCm39) |
I458T |
probably damaging |
Het |
| Brd4 |
G |
A |
17: 32,433,756 (GRCm39) |
T468I |
probably benign |
Het |
| Cdh23 |
T |
A |
10: 60,146,940 (GRCm39) |
D2774V |
possibly damaging |
Het |
| Cfdp1 |
T |
C |
8: 112,495,417 (GRCm39) |
Y267C |
probably damaging |
Het |
| Chd6 |
C |
A |
2: 160,803,211 (GRCm39) |
A2156S |
probably benign |
Het |
| Dazap2 |
C |
A |
15: 100,515,971 (GRCm39) |
P100T |
probably damaging |
Het |
| Disp1 |
T |
A |
1: 182,869,208 (GRCm39) |
I1071F |
possibly damaging |
Het |
| Dlgap1 |
T |
A |
17: 71,073,038 (GRCm39) |
S686T |
probably benign |
Het |
| Dst |
C |
T |
1: 34,231,421 (GRCm39) |
R3183C |
possibly damaging |
Het |
| Enpp4 |
T |
C |
17: 44,412,698 (GRCm39) |
N279D |
probably benign |
Het |
| Exoc3l |
T |
C |
8: 106,016,593 (GRCm39) |
*740W |
probably null |
Het |
| Exoc5 |
A |
T |
14: 49,252,937 (GRCm39) |
C625* |
probably null |
Het |
| Fam98b |
A |
T |
2: 117,090,712 (GRCm39) |
N137Y |
possibly damaging |
Het |
| Fat4 |
T |
A |
3: 38,945,776 (GRCm39) |
D1556E |
probably damaging |
Het |
| Fcer2a |
C |
A |
8: 3,732,848 (GRCm39) |
V319L |
possibly damaging |
Het |
| Fer1l6 |
T |
C |
15: 58,499,371 (GRCm39) |
V1247A |
probably benign |
Het |
| Fmo4 |
A |
G |
1: 162,632,748 (GRCm39) |
V201A |
probably damaging |
Het |
| Fras1 |
G |
A |
5: 96,762,763 (GRCm39) |
G755D |
probably benign |
Het |
| Grid2 |
T |
C |
6: 63,886,029 (GRCm39) |
Y142H |
probably damaging |
Het |
| Hspg2 |
C |
T |
4: 137,246,251 (GRCm39) |
R1010C |
probably damaging |
Het |
| Ibtk |
T |
C |
9: 85,608,784 (GRCm39) |
Q376R |
probably damaging |
Het |
| Impdh2 |
T |
C |
9: 108,442,155 (GRCm39) |
M414T |
probably damaging |
Het |
| Itm2c |
A |
G |
1: 85,834,750 (GRCm39) |
T160A |
probably damaging |
Het |
| Kcna2 |
T |
A |
3: 107,012,509 (GRCm39) |
D363E |
probably benign |
Het |
| Lama2 |
C |
T |
10: 27,223,050 (GRCm39) |
C412Y |
probably damaging |
Het |
| Lims2 |
C |
G |
18: 32,089,390 (GRCm39) |
T151S |
probably benign |
Het |
| Mier1 |
T |
C |
4: 103,019,628 (GRCm39) |
S423P |
possibly damaging |
Het |
| Mrgpra3 |
A |
T |
7: 47,239,180 (GRCm39) |
W249R |
probably benign |
Het |
| Mtor |
A |
G |
4: 148,634,609 (GRCm39) |
H2410R |
probably benign |
Het |
| Mvp |
C |
T |
7: 126,588,875 (GRCm39) |
A631T |
probably benign |
Het |
| Nepro |
T |
C |
16: 44,556,192 (GRCm39) |
V450A |
possibly damaging |
Het |
| Ngrn |
T |
C |
7: 79,914,269 (GRCm39) |
V140A |
probably damaging |
Het |
| Nobox |
T |
C |
6: 43,282,942 (GRCm39) |
E231G |
probably benign |
Het |
| Or10al7 |
A |
T |
17: 38,366,163 (GRCm39) |
I98N |
probably damaging |
Het |
| P3h2 |
T |
A |
16: 25,923,971 (GRCm39) |
I155F |
probably benign |
Het |
| Pramel24 |
A |
T |
4: 143,453,416 (GRCm39) |
K175* |
probably null |
Het |
| Riok3 |
AGAAGCGG |
AG |
18: 12,268,998 (GRCm39) |
|
probably benign |
Het |
| Rttn |
T |
C |
18: 89,110,020 (GRCm39) |
I1675T |
probably benign |
Het |
| Sall2 |
C |
A |
14: 52,551,260 (GRCm39) |
R643L |
probably damaging |
Het |
| Slc35f4 |
G |
T |
14: 49,541,758 (GRCm39) |
T182N |
possibly damaging |
Het |
| Slc52a3 |
T |
A |
2: 151,847,660 (GRCm39) |
I256N |
possibly damaging |
Het |
| Sox9 |
T |
C |
11: 112,675,980 (GRCm39) |
S390P |
possibly damaging |
Het |
| Tango2 |
T |
C |
16: 18,120,654 (GRCm39) |
|
probably benign |
Het |
| Tas1r1 |
T |
C |
4: 152,116,614 (GRCm39) |
E340G |
possibly damaging |
Het |
| Tek |
G |
A |
4: 94,718,207 (GRCm39) |
G524R |
probably damaging |
Het |
| Tmem260 |
A |
T |
14: 48,742,761 (GRCm39) |
Y532F |
probably benign |
Het |
| Tsks |
C |
A |
7: 44,607,353 (GRCm39) |
L559I |
probably damaging |
Het |
| Unc79 |
C |
A |
12: 103,088,612 (GRCm39) |
L1702I |
probably damaging |
Het |
| Vmn1r14 |
T |
A |
6: 57,211,133 (GRCm39) |
I237N |
probably damaging |
Het |
| Vmn2r17 |
G |
A |
5: 109,600,832 (GRCm39) |
C710Y |
probably benign |
Het |
| Zfp119b |
G |
T |
17: 56,245,926 (GRCm39) |
T420K |
possibly damaging |
Het |
| Zfp202 |
C |
T |
9: 40,118,790 (GRCm39) |
R68* |
probably null |
Het |
| Zfp229 |
T |
A |
17: 21,965,802 (GRCm39) |
S677R |
probably benign |
Het |
| Zfp462 |
C |
T |
4: 55,008,411 (GRCm39) |
H126Y |
probably benign |
Het |
| Zfp52 |
C |
A |
17: 21,780,459 (GRCm39) |
Y102* |
probably null |
Het |
| Zfp616 |
T |
A |
11: 73,974,526 (GRCm39) |
M265K |
probably benign |
Het |
| Zfyve9 |
A |
T |
4: 108,538,173 (GRCm39) |
I1031N |
probably damaging |
Het |
| Zmynd11 |
T |
C |
13: 9,747,726 (GRCm39) |
Y203C |
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 |
|
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'- ATGAGAACGACAATGCGCC -3'
(R):5'- GATGGCGATGATCAGGTACAC -3'
Sequencing Primer
(F):5'- AATGCGCCCACACTGCTG -3'
(R):5'- CAGGTACACGTTGATATCTACAAGCG -3'
|
| Posted On |
2015-06-20 |
Incidental Mutation