Incidental Mutation 'R4154:Pcdha4'
| ID |
315065 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha4
|
| Ensembl Gene |
ENSMUSG00000104252 |
| Gene Name |
protocadherin alpha 4 |
| Synonyms |
Crnr1, Cnr1 |
| MMRRC Submission |
040998-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.172)
|
| Stock # |
R4154 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
37085742-37320710 bp(+) (GRCm39) |
| Type of Mutation |
splice site (20914 bp from exon) |
| DNA Base Change (assembly) |
A to G
at 37086639 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000142308
(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 null
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 damaging
Transcript: ENSMUST00000115661
AA Change: N274S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458
AA Change: N274S
| 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 damaging
Transcript: ENSMUST00000192295
AA Change: N274S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000142103
Gene: ENSMUSG00000104252
AA Change: N274S
| 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 null
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 damaging
Transcript: ENSMUST00000192512
AA Change: N274S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000141408
Gene: ENSMUSG00000104252
AA Change: N274S
| 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 null
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 |
|
| Meta Mutation Damage Score |
0.9482 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.5%
|
| Validation Efficiency |
98% (51/52) |
| 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: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| AI593442 |
A |
T |
9: 52,589,204 (GRCm39) |
H124Q |
probably benign |
Het |
| Asph |
C |
T |
4: 9,639,250 (GRCm39) |
W38* |
probably null |
Het |
| Bicdl2 |
A |
G |
17: 23,885,066 (GRCm39) |
|
probably null |
Het |
| Chd8 |
T |
C |
14: 52,444,668 (GRCm39) |
|
probably benign |
Het |
| Clcn4 |
T |
C |
7: 7,297,833 (GRCm39) |
N67D |
probably benign |
Het |
| Cptp |
A |
G |
4: 155,951,657 (GRCm39) |
V12A |
possibly damaging |
Het |
| Crim1 |
A |
G |
17: 78,545,272 (GRCm39) |
I145V |
probably benign |
Het |
| Ctsc |
G |
A |
7: 87,948,755 (GRCm39) |
M195I |
probably benign |
Het |
| Ddx41 |
G |
A |
13: 55,682,293 (GRCm39) |
R205W |
possibly damaging |
Het |
| Fas |
T |
G |
19: 34,296,228 (GRCm39) |
I180S |
possibly damaging |
Het |
| Fsip2 |
A |
C |
2: 82,817,413 (GRCm39) |
E4382A |
possibly damaging |
Het |
| Galnt5 |
T |
G |
2: 57,888,505 (GRCm39) |
L35R |
probably damaging |
Het |
| Gfpt2 |
G |
A |
11: 49,726,605 (GRCm39) |
|
probably null |
Het |
| Gjd4 |
G |
T |
18: 9,280,811 (GRCm39) |
S89* |
probably null |
Het |
| Gm14496 |
A |
T |
2: 181,636,872 (GRCm39) |
H110L |
probably benign |
Het |
| Golm1 |
A |
G |
13: 59,790,167 (GRCm39) |
V211A |
probably benign |
Het |
| Gsc2 |
TGCAGCAGCAGCAGCAG |
TGCAGCAGCAGCAG |
16: 17,732,666 (GRCm39) |
|
probably benign |
Het |
| Ighv1-72 |
A |
T |
12: 115,722,017 (GRCm39) |
M7K |
probably benign |
Het |
| Igkv12-44 |
C |
T |
6: 69,791,639 (GRCm39) |
C108Y |
possibly damaging |
Het |
| Lum |
T |
C |
10: 97,404,815 (GRCm39) |
S237P |
probably damaging |
Het |
| Macf1 |
T |
C |
4: 123,365,606 (GRCm39) |
K3052E |
probably damaging |
Het |
| Mdn1 |
A |
G |
4: 32,707,475 (GRCm39) |
E1588G |
probably damaging |
Het |
| Ndst3 |
T |
C |
3: 123,465,876 (GRCm39) |
Y32C |
probably damaging |
Het |
| Nucb2 |
A |
G |
7: 116,126,902 (GRCm39) |
T172A |
probably benign |
Het |
| Or52b1 |
T |
C |
7: 104,978,592 (GRCm39) |
N269S |
probably damaging |
Het |
| Pard3 |
G |
T |
8: 128,200,877 (GRCm39) |
R978L |
probably damaging |
Het |
| Pgk2 |
A |
G |
17: 40,519,149 (GRCm39) |
V93A |
probably damaging |
Het |
| Pik3c3 |
G |
A |
18: 30,444,336 (GRCm39) |
M516I |
probably benign |
Het |
| Plxnb2 |
A |
G |
15: 89,043,845 (GRCm39) |
F1336L |
probably damaging |
Het |
| Shroom3 |
G |
T |
5: 93,090,945 (GRCm39) |
V1151F |
probably damaging |
Het |
| Sipa1l1 |
G |
C |
12: 82,471,988 (GRCm39) |
G1323R |
possibly damaging |
Het |
| Sntg1 |
A |
T |
1: 8,653,569 (GRCm39) |
|
probably null |
Het |
| Spef2 |
T |
C |
15: 9,626,107 (GRCm39) |
K1153R |
probably benign |
Het |
| Strn3 |
C |
T |
12: 51,673,914 (GRCm39) |
V566M |
probably damaging |
Het |
| Svep1 |
A |
G |
4: 58,069,068 (GRCm39) |
F2906S |
possibly damaging |
Het |
| Tbc1d8 |
C |
T |
1: 39,425,216 (GRCm39) |
V545M |
probably damaging |
Het |
| Tmem131 |
T |
C |
1: 36,847,874 (GRCm39) |
|
probably benign |
Het |
| Tnfsf8 |
A |
G |
4: 63,752,595 (GRCm39) |
S157P |
probably benign |
Het |
| Tubgcp5 |
G |
A |
7: 55,455,077 (GRCm39) |
V258M |
probably benign |
Het |
| Vat1l |
G |
C |
8: 114,932,543 (GRCm39) |
G30R |
possibly damaging |
Het |
| Vegfb |
T |
C |
19: 6,963,446 (GRCm39) |
Y106C |
probably damaging |
Het |
| Vmn2r100 |
AAAACAGGAGTATTGATTGGAAAC |
AAAAC |
17: 19,743,681 (GRCm39) |
|
probably null |
Het |
| Zc3h15 |
T |
C |
2: 83,488,913 (GRCm39) |
V161A |
probably benign |
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 |
|
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 |
|
R5540:Pcdha4
|
UTSW |
18 |
37,087,890 (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'- ACGGAAATCTTTAGACCGGGAG -3'
(R):5'- ACTTTACAGTGCCCAGAGAGTG -3'
Sequencing Primer
(F):5'- AGTGCTTACTGTCACGGAC -3'
(R):5'- GGAAGTTGTCCCTTGTCAATTC -3'
|
| Posted On |
2015-05-14 |
Incidental Mutation