Incidental Mutation 'R7659:Pcdha3'
| ID |
591468 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha3
|
| Ensembl Gene |
ENSMUSG00000102312 |
| Gene Name |
protocadherin alpha 3 |
| Synonyms |
|
| MMRRC Submission |
045734-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.111)
|
| Stock # |
R7659 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
37079158-37320710 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 37081219 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Alanine
at position 654
(T654A)
|
| 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: T654A
PolyPhen 2
Score 0.144 (Sensitivity: 0.92; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000141989
Gene: ENSMUSG00000102312
AA Change: T654A
| 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: 99.9%
- 10x: 99.7%
- 20x: 99.2%
|
| Validation Efficiency |
100% (66/66) |
| 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: 66 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aldh2 |
T |
C |
5: 121,707,023 (GRCm39) |
E498G |
probably damaging |
Het |
| Ankar |
T |
C |
1: 72,729,294 (GRCm39) |
T284A |
possibly damaging |
Het |
| Arid5b |
C |
T |
10: 67,934,417 (GRCm39) |
G495E |
probably benign |
Het |
| Armh1 |
C |
A |
4: 117,070,938 (GRCm39) |
A396S |
probably benign |
Het |
| Atp6v0a4 |
A |
G |
6: 38,048,907 (GRCm39) |
I452T |
probably damaging |
Het |
| Azgp1 |
G |
T |
5: 137,985,775 (GRCm39) |
A133S |
probably damaging |
Het |
| Bmp2k |
T |
C |
5: 97,222,578 (GRCm39) |
S667P |
unknown |
Het |
| C1qtnf9 |
T |
A |
14: 61,009,753 (GRCm39) |
I3N |
possibly damaging |
Het |
| C530025M09Rik |
T |
G |
2: 149,672,539 (GRCm39) |
T199P |
unknown |
Het |
| Casc3 |
C |
G |
11: 98,700,699 (GRCm39) |
R4G |
unknown |
Het |
| Cass4 |
A |
G |
2: 172,268,947 (GRCm39) |
D343G |
probably damaging |
Het |
| Cenatac |
T |
C |
9: 44,324,790 (GRCm39) |
E164G |
probably damaging |
Het |
| Col6a3 |
T |
A |
1: 90,709,467 (GRCm39) |
T2517S |
unknown |
Het |
| Dbr1 |
A |
G |
9: 99,458,663 (GRCm39) |
T78A |
probably damaging |
Het |
| Dnah9 |
A |
G |
11: 65,880,606 (GRCm39) |
F2664L |
probably damaging |
Het |
| Eif2ak1 |
T |
C |
5: 143,826,280 (GRCm39) |
I431T |
probably damaging |
Het |
| Got1 |
A |
G |
19: 43,493,078 (GRCm39) |
V281A |
probably benign |
Het |
| Gpld1 |
A |
C |
13: 25,163,964 (GRCm39) |
R555S |
probably benign |
Het |
| Gpr149 |
T |
C |
3: 62,511,256 (GRCm39) |
R248G |
probably benign |
Het |
| Hps3 |
G |
A |
3: 20,076,978 (GRCm39) |
R395* |
probably null |
Het |
| Inpp5b |
T |
C |
4: 124,689,219 (GRCm39) |
L833P |
probably damaging |
Het |
| Itgb4 |
A |
T |
11: 115,870,557 (GRCm39) |
S129C |
probably damaging |
Het |
| Kif1a |
T |
A |
1: 92,974,542 (GRCm39) |
|
probably benign |
Het |
| Lgr4 |
T |
A |
2: 109,827,111 (GRCm39) |
V205E |
probably damaging |
Het |
| Mbd3 |
T |
C |
10: 80,231,019 (GRCm39) |
N96S |
probably damaging |
Het |
| Mcam |
T |
A |
9: 44,048,067 (GRCm39) |
C136S |
unknown |
Het |
| Mki67 |
A |
G |
7: 135,299,155 (GRCm39) |
S1960P |
probably damaging |
Het |
| Mogs |
G |
A |
6: 83,093,806 (GRCm39) |
|
probably null |
Het |
| Muc6 |
T |
C |
7: 141,216,973 (GRCm39) |
T2567A |
possibly damaging |
Het |
| Mug1 |
C |
A |
6: 121,838,179 (GRCm39) |
H470N |
possibly damaging |
Het |
| Nae1 |
A |
G |
8: 105,242,796 (GRCm39) |
V432A |
probably benign |
Het |
| Nav3 |
T |
G |
10: 109,602,851 (GRCm39) |
T1233P |
probably benign |
Het |
| Nme9 |
G |
A |
9: 99,352,910 (GRCm39) |
A287T |
possibly damaging |
Het |
| Nmrk1 |
A |
G |
19: 18,613,499 (GRCm39) |
I8V |
probably benign |
Het |
| Noa1 |
T |
C |
5: 77,457,237 (GRCm39) |
N223D |
not run |
Het |
| Nr4a3 |
T |
C |
4: 48,051,269 (GRCm39) |
Y8H |
probably damaging |
Het |
| Or12e1 |
T |
A |
2: 87,022,709 (GRCm39) |
V226E |
possibly damaging |
Het |
| Or1j15 |
T |
A |
2: 36,458,637 (GRCm39) |
V9E |
possibly damaging |
Het |
| Or2b4 |
A |
T |
17: 38,116,054 (GRCm39) |
Q6L |
probably benign |
Het |
| Or4n4b |
T |
C |
14: 50,536,698 (GRCm39) |
I23V |
probably benign |
Het |
| Or4p20 |
T |
C |
2: 88,254,270 (GRCm39) |
Y33C |
probably damaging |
Het |
| Or52h2 |
T |
C |
7: 103,839,394 (GRCm39) |
S7G |
probably benign |
Het |
| Or7g29 |
C |
T |
9: 19,286,854 (GRCm39) |
A108T |
probably benign |
Het |
| Or8c9 |
T |
C |
9: 38,241,012 (GRCm39) |
V40A |
possibly damaging |
Het |
| Otoa |
T |
A |
7: 120,733,267 (GRCm39) |
H711Q |
probably benign |
Het |
| Otogl |
T |
A |
10: 107,612,981 (GRCm39) |
E2048D |
probably benign |
Het |
| Paip1 |
C |
T |
13: 119,587,306 (GRCm39) |
T390I |
possibly damaging |
Het |
| Pigg |
G |
A |
5: 108,486,485 (GRCm39) |
V713I |
probably benign |
Het |
| Ppt1 |
T |
A |
4: 122,730,126 (GRCm39) |
H26Q |
probably benign |
Het |
| Prim1 |
T |
C |
10: 127,862,458 (GRCm39) |
|
probably null |
Het |
| Prmt7 |
G |
T |
8: 106,963,918 (GRCm39) |
A271S |
probably benign |
Het |
| Ptprd |
T |
C |
4: 76,047,153 (GRCm39) |
D124G |
probably benign |
Het |
| Rad54l2 |
T |
C |
9: 106,590,777 (GRCm39) |
K450E |
probably benign |
Het |
| Rasgrp2 |
G |
T |
19: 6,451,857 (GRCm39) |
V13L |
probably damaging |
Het |
| Sapcd2 |
A |
G |
2: 25,265,978 (GRCm39) |
|
probably null |
Het |
| Siglecf |
A |
G |
7: 43,001,194 (GRCm39) |
Y54C |
probably damaging |
Het |
| Stk31 |
T |
A |
6: 49,400,340 (GRCm39) |
N388K |
probably benign |
Het |
| Timm23 |
A |
C |
14: 31,920,935 (GRCm39) |
Y52* |
probably null |
Het |
| Tm9sf1 |
A |
T |
14: 55,873,792 (GRCm39) |
F569I |
probably damaging |
Het |
| Tmprss9 |
C |
A |
10: 80,728,843 (GRCm39) |
A592E |
probably damaging |
Het |
| Trim30d |
A |
T |
7: 104,121,554 (GRCm39) |
V397E |
probably benign |
Het |
| Tshz1 |
A |
T |
18: 84,034,200 (GRCm39) |
N69K |
probably damaging |
Het |
| Upk2 |
A |
C |
9: 44,364,808 (GRCm39) |
S130R |
probably damaging |
Het |
| Vmn1r80 |
A |
G |
7: 11,926,977 (GRCm39) |
Y29C |
probably damaging |
Het |
| Vmn2r96 |
T |
C |
17: 18,793,749 (GRCm39) |
I31T |
probably benign |
Het |
| Zfp975 |
T |
C |
7: 42,311,848 (GRCm39) |
Q255R |
probably benign |
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 |
|
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'- ACGCGTGGCTCTCTTATGAG -3'
(R):5'- ATATGACCAGGTCCCCACTG -3'
Sequencing Primer
(F):5'- TCTCTTATGAGCTGCAGTCAG -3'
(R):5'- CACCTGAGTGCAAGGTACAGC -3'
|
| Posted On |
2019-11-12 |
Incidental Mutation