Incidental Mutation 'R5931:Pcdha4'
ID |
461882 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Pcdha4
|
Ensembl Gene |
ENSMUSG00000104252 |
Gene Name |
protocadherin alpha 4 |
Synonyms |
Crnr1, Cnr1 |
MMRRC Submission |
044126-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.161)
|
Stock # |
R5931 (G1)
|
Quality Score |
225 |
Status
|
Not validated
|
Chromosome |
18 |
Chromosomal Location |
37085742-37320710 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 37087808 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Threonine to Serine
at position 664
(T664S)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000141408
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000070797]
[ENSMUST00000115661]
[ENSMUST00000115662]
[ENSMUST00000192295]
[ENSMUST00000192503]
[ENSMUST00000192512]
[ENSMUST00000195590]
[ENSMUST00000193839]
|
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: T664S
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000111325 Gene: ENSMUSG00000103458 AA Change: T664S
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
|
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: T664S
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
SMART Domains |
Protein: ENSMUSP00000141408 Gene: ENSMUSG00000104252 AA Change: T664S
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 |
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 |
|
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 |
|
Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.1%
- 20x: 94.4%
|
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: 62 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4930590J08Rik |
A |
T |
6: 91,896,096 (GRCm39) |
R315W |
probably damaging |
Het |
Atrn |
A |
T |
2: 130,775,356 (GRCm39) |
Y153F |
possibly damaging |
Het |
C4b |
A |
G |
17: 34,948,167 (GRCm39) |
V1644A |
probably damaging |
Het |
Carmil3 |
A |
C |
14: 55,736,397 (GRCm39) |
K654T |
probably damaging |
Het |
Cdh1 |
T |
C |
8: 107,392,964 (GRCm39) |
|
probably null |
Het |
Chrna1 |
C |
T |
2: 73,398,444 (GRCm39) |
V332M |
probably benign |
Het |
Clca3a2 |
A |
C |
3: 144,797,886 (GRCm39) |
V193G |
possibly damaging |
Het |
Cyld |
A |
G |
8: 89,456,470 (GRCm39) |
|
probably null |
Het |
Dbt |
A |
T |
3: 116,317,074 (GRCm39) |
E83D |
possibly damaging |
Het |
Deup1 |
T |
C |
9: 15,472,618 (GRCm39) |
R471G |
possibly damaging |
Het |
Dgcr2 |
T |
A |
16: 17,675,173 (GRCm39) |
I188F |
possibly damaging |
Het |
Dgkg |
G |
A |
16: 22,376,788 (GRCm39) |
R524* |
probably null |
Het |
Dnaaf9 |
G |
A |
2: 130,656,109 (GRCm39) |
T2M |
probably damaging |
Het |
Dnah5 |
A |
T |
15: 28,453,425 (GRCm39) |
R4399W |
probably damaging |
Het |
Egflam |
G |
A |
15: 7,273,338 (GRCm39) |
T579I |
possibly damaging |
Het |
Eif2b2 |
C |
T |
12: 85,269,561 (GRCm39) |
T211I |
probably damaging |
Het |
Ep400 |
A |
G |
5: 110,883,386 (GRCm39) |
|
probably benign |
Het |
Ermp1 |
C |
G |
19: 29,593,129 (GRCm39) |
A788P |
probably benign |
Het |
Ern1 |
A |
G |
11: 106,317,699 (GRCm39) |
S142P |
possibly damaging |
Het |
Fbxo15 |
T |
A |
18: 84,999,250 (GRCm39) |
C351S |
probably damaging |
Het |
Fndc3a |
A |
T |
14: 72,806,307 (GRCm39) |
S444T |
probably benign |
Het |
Gabra6 |
G |
A |
11: 42,198,268 (GRCm39) |
T384M |
probably benign |
Het |
Gpbp1l1 |
T |
C |
4: 116,447,457 (GRCm39) |
V379A |
probably benign |
Het |
Hook2 |
G |
T |
8: 85,722,375 (GRCm39) |
E305* |
probably null |
Het |
Hoxa3 |
G |
A |
6: 52,149,568 (GRCm39) |
A21V |
probably damaging |
Het |
Hs1bp3 |
C |
A |
12: 8,391,915 (GRCm39) |
P339Q |
probably benign |
Het |
Igha |
T |
A |
12: 113,223,710 (GRCm39) |
T49S |
probably benign |
Het |
Klra4 |
C |
T |
6: 130,030,016 (GRCm39) |
V190M |
possibly damaging |
Het |
Lats2 |
A |
G |
14: 57,933,588 (GRCm39) |
L843P |
probably damaging |
Het |
Lcmt1 |
A |
G |
7: 123,020,839 (GRCm39) |
T255A |
probably benign |
Het |
Lpar6 |
A |
G |
14: 73,476,368 (GRCm39) |
I110V |
probably damaging |
Het |
Lrrtm4 |
A |
G |
6: 79,998,722 (GRCm39) |
I44V |
probably damaging |
Het |
Mcm3ap |
T |
C |
10: 76,307,000 (GRCm39) |
V371A |
probably benign |
Het |
Muc20 |
A |
T |
16: 32,614,944 (GRCm39) |
D144E |
possibly damaging |
Het |
Nphp3 |
T |
A |
9: 103,897,945 (GRCm39) |
D417E |
probably damaging |
Het |
Or7g33 |
A |
T |
9: 19,448,629 (GRCm39) |
I199K |
probably benign |
Het |
Or8b40 |
A |
G |
9: 38,027,670 (GRCm39) |
I193V |
probably benign |
Het |
Paqr7 |
A |
C |
4: 134,235,031 (GRCm39) |
Y296S |
probably damaging |
Het |
Pelo |
T |
A |
13: 115,225,379 (GRCm39) |
Y282F |
probably benign |
Het |
Plxna2 |
A |
T |
1: 194,493,178 (GRCm39) |
I1818F |
probably damaging |
Het |
Pnkd |
A |
G |
1: 74,389,833 (GRCm39) |
D319G |
probably benign |
Het |
Pnma8a |
C |
A |
7: 16,694,809 (GRCm39) |
N221K |
probably benign |
Het |
Ppp1cb |
T |
A |
5: 32,640,810 (GRCm39) |
|
probably null |
Het |
Prkca |
T |
G |
11: 107,905,136 (GRCm39) |
I201L |
probably benign |
Het |
Prp2rt |
A |
G |
13: 97,235,705 (GRCm39) |
L14S |
probably benign |
Het |
Rfx2 |
G |
A |
17: 57,087,778 (GRCm39) |
R538C |
probably damaging |
Het |
Rph3a |
T |
C |
5: 121,101,936 (GRCm39) |
Q100R |
probably damaging |
Het |
Rtel1 |
C |
T |
2: 180,972,608 (GRCm39) |
R29* |
probably null |
Het |
Scel |
T |
A |
14: 103,843,060 (GRCm39) |
Y547* |
probably null |
Het |
Sp100 |
C |
T |
1: 85,606,804 (GRCm39) |
P303L |
probably damaging |
Het |
Stk31 |
A |
G |
6: 49,446,236 (GRCm39) |
S958G |
probably benign |
Het |
Syne2 |
T |
A |
12: 76,055,639 (GRCm39) |
V4168E |
probably benign |
Het |
Tenm3 |
A |
T |
8: 49,099,533 (GRCm39) |
S91T |
probably benign |
Het |
Tmcc2 |
TTGCTGCTGCTGCTGCTGC |
TTGCTGCTGCTGCTGC |
1: 132,285,493 (GRCm39) |
|
probably benign |
Het |
Tmem248 |
T |
A |
5: 130,258,349 (GRCm39) |
I14N |
probably damaging |
Het |
Tor3a |
T |
C |
1: 156,484,057 (GRCm39) |
I298V |
probably benign |
Het |
Trim69 |
A |
T |
2: 122,009,075 (GRCm39) |
K378N |
probably damaging |
Het |
Ttc28 |
C |
T |
5: 111,232,975 (GRCm39) |
P151S |
possibly damaging |
Het |
Uaca |
T |
C |
9: 60,779,294 (GRCm39) |
V1225A |
probably damaging |
Het |
Vps4b |
T |
C |
1: 106,705,065 (GRCm39) |
I343V |
probably benign |
Het |
Wnk4 |
A |
G |
11: 101,152,047 (GRCm39) |
T184A |
probably damaging |
Het |
Ythdc2 |
T |
A |
18: 45,006,023 (GRCm39) |
I1172K |
possibly damaging |
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 |
|
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'- CTTATGAGCTGCAATCGTCAG -3'
(R):5'- CACACCATTACCGGTTTTGGAG -3'
Sequencing Primer
(F):5'- TCGTCAGAAGGCAATTCCCGTAG -3'
(R):5'- TTTTGGAGGCCCGCACAC -3'
|
Posted On |
2017-02-28 |