Incidental Mutation 'R5535:Pcdha3'
| ID |
434800 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha3
|
| Ensembl Gene |
ENSMUSG00000102312 |
| Gene Name |
protocadherin alpha 3 |
| Synonyms |
|
| MMRRC Submission |
043093-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.111)
|
| Stock # |
R5535 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
18 |
| Chromosomal Location |
37079158-37320710 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to T
at 37080989 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Leucine
at position 577
(R577L)
|
| 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: R577L
PolyPhen 2
Score 0.017 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000141989
Gene: ENSMUSG00000102312
AA Change: R577L
| 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: 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: 100.0%
- 3x: 99.9%
- 10x: 99.3%
- 20x: 97.6%
|
| 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: 39 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acaa1b |
C |
T |
9: 118,977,474 (GRCm39) |
G403S |
probably damaging |
Het |
| Agbl2 |
G |
A |
2: 90,640,350 (GRCm39) |
V699I |
probably benign |
Het |
| Amer2 |
AAGGAGGAGGAGGAG |
AAGGAGGAGGAG |
14: 60,616,302 (GRCm39) |
|
probably benign |
Het |
| Bace2 |
A |
T |
16: 97,214,625 (GRCm39) |
Q271L |
probably damaging |
Het |
| Btn2a2 |
T |
C |
13: 23,662,445 (GRCm39) |
K493E |
probably benign |
Het |
| Ces3a |
T |
A |
8: 105,778,196 (GRCm39) |
D222E |
probably benign |
Het |
| Ckap2l |
A |
G |
2: 129,127,762 (GRCm39) |
C139R |
probably benign |
Het |
| Clip4 |
A |
G |
17: 72,138,257 (GRCm39) |
H485R |
probably benign |
Het |
| Cntfr |
T |
A |
4: 41,663,216 (GRCm39) |
D197V |
probably benign |
Het |
| Efcab5 |
A |
G |
11: 77,042,747 (GRCm39) |
L2P |
probably damaging |
Het |
| Elmo2 |
A |
G |
2: 165,152,132 (GRCm39) |
V163A |
possibly damaging |
Het |
| Fkbpl |
G |
A |
17: 34,864,303 (GRCm39) |
A24T |
probably benign |
Het |
| Flrt2 |
A |
G |
12: 95,747,200 (GRCm39) |
T513A |
probably benign |
Het |
| Gm10801 |
GT |
GTTTTT |
2: 98,492,844 (GRCm39) |
|
probably null |
Het |
| Hectd1 |
A |
T |
12: 51,849,109 (GRCm39) |
F332I |
probably damaging |
Het |
| Helz |
A |
G |
11: 107,536,946 (GRCm39) |
D947G |
probably damaging |
Het |
| Hivep2 |
T |
A |
10: 14,006,766 (GRCm39) |
D1121E |
probably benign |
Het |
| Hoxa13 |
GG |
GGCG |
6: 52,237,520 (GRCm39) |
|
probably null |
Homo |
| Hoxd13 |
A |
T |
2: 74,499,141 (GRCm39) |
Y163F |
probably damaging |
Het |
| Immt |
C |
A |
6: 71,829,768 (GRCm39) |
P158Q |
probably null |
Het |
| Kcnh5 |
A |
G |
12: 75,177,681 (GRCm39) |
S142P |
possibly damaging |
Het |
| Lnpep |
T |
G |
17: 17,758,956 (GRCm39) |
H796P |
probably benign |
Het |
| Mfhas1 |
C |
A |
8: 36,057,423 (GRCm39) |
R633S |
possibly damaging |
Het |
| Mmp25 |
A |
G |
17: 23,863,734 (GRCm39) |
L32P |
probably benign |
Het |
| Myo15b |
A |
G |
11: 115,772,127 (GRCm39) |
D299G |
probably damaging |
Het |
| Myo18b |
T |
C |
5: 112,937,908 (GRCm39) |
E1739G |
probably damaging |
Het |
| Or8b44 |
T |
A |
9: 38,410,294 (GRCm39) |
S110T |
probably benign |
Het |
| Parp9 |
A |
G |
16: 35,777,195 (GRCm39) |
K147E |
probably damaging |
Het |
| Plod2 |
T |
A |
9: 92,488,622 (GRCm39) |
I637N |
probably damaging |
Het |
| Polk |
T |
G |
13: 96,632,005 (GRCm39) |
S243R |
probably damaging |
Het |
| Prag1 |
T |
C |
8: 36,571,168 (GRCm39) |
S584P |
probably benign |
Het |
| Prex1 |
A |
T |
2: 166,422,193 (GRCm39) |
V43E |
possibly damaging |
Het |
| Rdh10 |
T |
C |
1: 16,201,408 (GRCm39) |
Y294H |
probably damaging |
Het |
| Rnf126 |
T |
A |
10: 79,598,533 (GRCm39) |
I28F |
probably damaging |
Het |
| Sdk2 |
T |
A |
11: 113,833,984 (GRCm39) |
H66L |
possibly damaging |
Het |
| Tet1 |
G |
T |
10: 62,668,686 (GRCm39) |
P1431Q |
probably damaging |
Het |
| Tmco2 |
T |
A |
4: 120,963,190 (GRCm39) |
Q103L |
possibly damaging |
Het |
| Ucp3 |
A |
T |
7: 100,129,873 (GRCm39) |
R172W |
probably benign |
Het |
| Unc79 |
A |
T |
12: 103,135,962 (GRCm39) |
I2270F |
possibly 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 |
|
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'- TGCTGTCGAGCTATGTGTCC -3'
(R):5'- TTTCATCCAGGACACGTGTG -3'
Sequencing Primer
(F):5'- AGCTATGTGTCCGTGCAC -3'
(R):5'- CACGTGTGGTGCTGATCTCAC -3'
|
| Posted On |
2016-10-24 |
Incidental Mutation