Incidental Mutation 'R8239:Pcdha4'
ID |
637534 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Pcdha4
|
Ensembl Gene |
ENSMUSG00000104252 |
Gene Name |
protocadherin alpha 4 |
Synonyms |
Crnr1, Cnr1 |
MMRRC Submission |
067646-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.161)
|
Stock # |
R8239 (G1)
|
Quality Score |
225.009 |
Status
|
Not validated
|
Chromosome |
18 |
Chromosomal Location |
37085742-37320710 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 37086128 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Isoleucine to Phenylalanine
at position 104
(I104F)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000141408
(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 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 damaging
Transcript: ENSMUST00000115661
AA Change: I104F
PolyPhen 2
Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)
|
SMART Domains |
Protein: ENSMUSP00000111325 Gene: ENSMUSG00000103458 AA Change: I104F
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: I104F
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000142103 Gene: ENSMUSG00000104252 AA Change: I104F
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
|
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: I104F
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000141408 Gene: ENSMUSG00000104252 AA Change: I104F
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: 99.9%
- 3x: 99.8%
- 10x: 99.5%
- 20x: 98.9%
|
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: 53 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adam39 |
T |
C |
8: 41,278,106 (GRCm39) |
S166P |
probably damaging |
Het |
Appl1 |
T |
A |
14: 26,686,914 (GRCm39) |
T19S |
probably damaging |
Het |
Arid4b |
T |
A |
13: 14,344,594 (GRCm39) |
D557E |
probably benign |
Het |
Aven |
C |
T |
2: 112,390,120 (GRCm39) |
R8W |
probably benign |
Het |
C2cd2l |
T |
C |
9: 44,227,502 (GRCm39) |
E307G |
possibly damaging |
Het |
Cdh20 |
A |
C |
1: 110,027,832 (GRCm39) |
T526P |
probably benign |
Het |
Dchs1 |
C |
T |
7: 105,414,718 (GRCm39) |
V775M |
probably benign |
Het |
Dennd1b |
A |
G |
1: 138,969,673 (GRCm39) |
N63S |
probably benign |
Het |
Dtnb |
A |
T |
12: 3,694,056 (GRCm39) |
Y248F |
unknown |
Het |
Ehbp1l1 |
T |
A |
19: 5,770,089 (GRCm39) |
T405S |
possibly damaging |
Het |
Fam149a |
A |
G |
8: 45,803,490 (GRCm39) |
Y415H |
possibly damaging |
Het |
Fam186a |
A |
G |
15: 99,839,191 (GRCm39) |
L2351P |
unknown |
Het |
Fsip2 |
T |
G |
2: 82,819,687 (GRCm39) |
I5140S |
possibly damaging |
Het |
Gm8674 |
T |
C |
13: 50,054,262 (GRCm39) |
T749A |
noncoding transcript |
Het |
Kalrn |
A |
G |
16: 33,870,153 (GRCm39) |
V1894A |
noncoding transcript |
Het |
Kpna3 |
A |
T |
14: 61,624,919 (GRCm39) |
N141K |
probably damaging |
Het |
Lrba |
G |
A |
3: 86,449,882 (GRCm39) |
G2067D |
probably damaging |
Het |
Lrp2 |
G |
T |
2: 69,311,611 (GRCm39) |
Y2622* |
probably null |
Het |
Lrtm2 |
A |
C |
6: 119,297,778 (GRCm39) |
F88V |
probably damaging |
Het |
Mboat1 |
T |
C |
13: 30,429,333 (GRCm39) |
S454P |
probably damaging |
Het |
Nkpd1 |
C |
T |
7: 19,253,753 (GRCm39) |
P40S |
probably benign |
Het |
Or2b7 |
T |
C |
13: 21,739,788 (GRCm39) |
I135V |
probably benign |
Het |
Or4a76 |
T |
A |
2: 89,460,907 (GRCm39) |
I112F |
probably damaging |
Het |
Or8b54 |
G |
A |
9: 38,686,577 (GRCm39) |
V9M |
noncoding transcript |
Het |
Or8k27 |
C |
A |
2: 86,275,473 (GRCm39) |
M284I |
noncoding transcript |
Het |
Patj |
A |
G |
4: 98,570,308 (GRCm39) |
E1711G |
possibly damaging |
Het |
Peg10 |
GC |
GCTCC |
6: 4,756,452 (GRCm39) |
|
probably benign |
Het |
Plekhg4 |
C |
T |
8: 106,107,546 (GRCm39) |
R990* |
probably null |
Het |
Pphln1 |
T |
C |
15: 93,386,930 (GRCm39) |
S343P |
probably benign |
Het |
Pram1 |
A |
T |
17: 33,860,241 (GRCm39) |
K269N |
probably damaging |
Het |
Psmd13 |
T |
A |
7: 140,466,450 (GRCm39) |
I79K |
probably damaging |
Het |
Ptprf |
T |
C |
4: 118,069,309 (GRCm39) |
D1586G |
possibly damaging |
Het |
Ptprh |
T |
A |
7: 4,584,090 (GRCm39) |
Q167H |
probably damaging |
Het |
Rbm46 |
C |
T |
3: 82,772,775 (GRCm39) |
R119Q |
probably benign |
Het |
Rreb1 |
T |
C |
13: 38,077,848 (GRCm39) |
M20T |
probably damaging |
Het |
Scrn2 |
T |
G |
11: 96,923,046 (GRCm39) |
L163R |
probably damaging |
Het |
Slc36a3 |
C |
T |
11: 55,022,433 (GRCm39) |
V254I |
probably benign |
Het |
Slc6a6 |
T |
C |
6: 91,701,951 (GRCm39) |
F120L |
probably benign |
Het |
Slc8a2 |
A |
T |
7: 15,879,230 (GRCm39) |
H572L |
probably benign |
Het |
Spats2 |
T |
A |
15: 99,106,776 (GRCm39) |
D357E |
probably damaging |
Het |
Speg |
A |
T |
1: 75,395,677 (GRCm39) |
N1816I |
probably damaging |
Het |
Sult2b1 |
A |
G |
7: 45,433,361 (GRCm39) |
V2A |
unknown |
Het |
Susd3 |
T |
C |
13: 49,384,731 (GRCm39) |
T231A |
probably benign |
Het |
Tamalin |
C |
T |
15: 101,128,902 (GRCm39) |
L217F |
probably damaging |
Het |
Tcp1 |
A |
G |
17: 13,139,738 (GRCm39) |
D261G |
probably benign |
Het |
Trpm2 |
C |
G |
10: 77,771,836 (GRCm39) |
S601T |
probably benign |
Het |
Ugt2b38 |
A |
T |
5: 87,571,659 (GRCm39) |
F124L |
probably benign |
Het |
Unc80 |
G |
T |
1: 66,693,178 (GRCm39) |
E2522D |
probably benign |
Het |
Usp34 |
A |
G |
11: 23,396,750 (GRCm39) |
T2365A |
|
Het |
Vmn2r92 |
G |
T |
17: 18,405,278 (GRCm39) |
M807I |
probably benign |
Het |
Vps13b |
C |
A |
15: 35,597,550 (GRCm39) |
P1030Q |
probably damaging |
Het |
Wrn |
T |
G |
8: 33,819,213 (GRCm39) |
K246N |
probably damaging |
Het |
Zer1 |
T |
A |
2: 29,991,147 (GRCm39) |
|
probably null |
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 |
R4154:Pcdha4
|
UTSW |
18 |
37,086,639 (GRCm39) |
splice site |
probably null |
|
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 |
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'- ATCCACTACTCCATCCCTGAGG -3'
(R):5'- TGATTCCGATATCTGCGTCTGAAG -3'
Sequencing Primer
(F):5'- TCCCTGAGGAGGCCAAAC -3'
(R):5'- TGAAGCGCCCTCTAGTGGAAAC -3'
|
Posted On |
2020-07-13 |