Incidental Mutation 'R6878:Pcdha3'
| ID |
536537 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdha3
|
| Ensembl Gene |
ENSMUSG00000102312 |
| Gene Name |
protocadherin alpha 3 |
| Synonyms |
|
| MMRRC Submission |
044974-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.111)
|
| Stock # |
R6878 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
37079158-37320710 bp(+) (GRCm39) |
| Type of Mutation |
nonsense |
| DNA Base Change (assembly) |
T to A
at 37080416 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Stop codon
at position 386
(L386*)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000141989
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000070797]
[ENSMUST00000115662]
[ENSMUST00000192503]
[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: 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 null
Transcript: ENSMUST00000192503
AA Change: L386*
|
| SMART Domains |
Protein: ENSMUSP00000141989
Gene: ENSMUSG00000102312
AA Change: L386*
| 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: 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 |
|
| Meta Mutation Damage Score |
0.9755 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.3%
- 20x: 97.7%
|
| Validation Efficiency |
98% (44/45) |
| 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: 48 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adgrv1 |
A |
T |
13: 81,581,613 (GRCm39) |
N4810K |
probably benign |
Het |
| Arhgap26 |
A |
T |
18: 39,360,465 (GRCm39) |
I397F |
probably damaging |
Het |
| Arhgap35 |
A |
G |
7: 16,299,038 (GRCm39) |
V9A |
probably benign |
Het |
| Asl |
A |
G |
5: 130,053,133 (GRCm39) |
|
probably null |
Het |
| Atg2a |
T |
A |
19: 6,300,208 (GRCm39) |
L672Q |
probably damaging |
Het |
| B4galt1 |
T |
C |
4: 40,809,694 (GRCm39) |
D316G |
probably damaging |
Het |
| Bpifb2 |
A |
G |
2: 153,717,832 (GRCm39) |
|
probably benign |
Het |
| Ccl1 |
T |
C |
11: 82,070,519 (GRCm39) |
I18V |
probably benign |
Het |
| Cd47 |
A |
G |
16: 49,731,232 (GRCm39) |
E278G |
possibly damaging |
Het |
| Cilp |
G |
A |
9: 65,187,129 (GRCm39) |
G1075S |
probably damaging |
Het |
| Eml2 |
T |
C |
7: 18,934,537 (GRCm39) |
V604A |
probably benign |
Het |
| Fancm |
A |
T |
12: 65,163,197 (GRCm39) |
R1454* |
probably null |
Het |
| Gm4302 |
TGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA |
TGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA |
10: 100,177,361 (GRCm39) |
|
probably benign |
Het |
| Gm4302 |
GCA |
GCACCA |
10: 100,177,377 (GRCm39) |
|
probably benign |
Het |
| Gm4302 |
CAG |
CAGAAG |
10: 100,177,369 (GRCm39) |
|
probably benign |
Het |
| Hif1a |
T |
C |
12: 73,975,055 (GRCm39) |
M147T |
possibly damaging |
Het |
| Hps5 |
C |
G |
7: 46,433,058 (GRCm39) |
A221P |
probably damaging |
Het |
| Lrrc49 |
A |
G |
9: 60,587,431 (GRCm39) |
S67P |
probably damaging |
Het |
| Madd |
T |
A |
2: 91,000,202 (GRCm39) |
N568I |
probably damaging |
Het |
| Meikin |
T |
C |
11: 54,302,712 (GRCm39) |
S375P |
possibly damaging |
Het |
| Mfsd6 |
G |
T |
1: 52,747,912 (GRCm39) |
Q318K |
probably damaging |
Het |
| Mis18a |
A |
T |
16: 90,518,644 (GRCm39) |
I106N |
probably damaging |
Het |
| Myl2 |
T |
C |
5: 122,243,140 (GRCm39) |
I148T |
probably benign |
Het |
| Myrf |
T |
C |
19: 10,193,842 (GRCm39) |
Q730R |
possibly damaging |
Het |
| Nf1 |
T |
C |
11: 79,325,708 (GRCm39) |
L560P |
probably damaging |
Het |
| Npat |
A |
G |
9: 53,467,899 (GRCm39) |
T285A |
probably benign |
Het |
| Ntrk3 |
T |
A |
7: 77,954,120 (GRCm39) |
D547V |
probably benign |
Het |
| Obox2 |
G |
T |
7: 15,131,245 (GRCm39) |
S117I |
probably benign |
Het |
| Or8k32 |
A |
G |
2: 86,369,109 (GRCm39) |
L48P |
probably damaging |
Het |
| Parva |
T |
A |
7: 112,175,656 (GRCm39) |
N226K |
possibly damaging |
Het |
| Ppip5k1 |
A |
G |
2: 121,142,417 (GRCm39) |
F1323S |
probably benign |
Het |
| Prkdc |
T |
C |
16: 15,594,936 (GRCm39) |
V2771A |
probably benign |
Het |
| Prl7c1 |
T |
C |
13: 27,962,827 (GRCm39) |
T59A |
possibly damaging |
Het |
| Rab15 |
T |
C |
12: 76,851,257 (GRCm39) |
T20A |
probably benign |
Het |
| Rp1l1 |
A |
G |
14: 64,269,301 (GRCm39) |
E1629G |
probably benign |
Het |
| Rpap1 |
A |
T |
2: 119,608,657 (GRCm39) |
L235Q |
probably damaging |
Het |
| Sema3a |
A |
T |
5: 13,505,511 (GRCm39) |
I91F |
possibly damaging |
Het |
| Snx6 |
T |
C |
12: 54,810,386 (GRCm39) |
|
probably null |
Het |
| Sorbs1 |
G |
C |
19: 40,365,244 (GRCm39) |
R180G |
probably benign |
Het |
| Speer4f2 |
T |
G |
5: 17,580,765 (GRCm39) |
M114R |
probably damaging |
Het |
| Syne1 |
T |
C |
10: 5,370,388 (GRCm39) |
D264G |
possibly damaging |
Het |
| Tbl1xr1 |
T |
G |
3: 22,257,368 (GRCm39) |
N410K |
possibly damaging |
Het |
| Tmed7 |
A |
T |
18: 46,726,532 (GRCm39) |
D74E |
probably damaging |
Het |
| Upk3b |
T |
C |
5: 136,068,001 (GRCm39) |
V64A |
probably benign |
Het |
| Vmn2r29 |
A |
G |
7: 7,244,863 (GRCm39) |
V337A |
probably benign |
Het |
| Yy1 |
C |
G |
12: 108,780,682 (GRCm39) |
P352A |
probably damaging |
Het |
| Zfp1005 |
C |
T |
2: 150,108,406 (GRCm39) |
L56F |
possibly damaging |
Het |
| Zfp873 |
T |
C |
10: 81,896,529 (GRCm39) |
I457T |
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 |
|
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'- CAGATCATTGCACGGTTCTAGTTG -3'
(R):5'- ACAAACACTGTGTACTCCGGC -3'
Sequencing Primer
(F):5'- CATTGCACGGTTCTAGTTGAAATTG -3'
(R):5'- GCAGGAGCATTGTCATTCAC -3'
|
| Posted On |
2018-10-18 |
Incidental Mutation