Incidental Mutation 'R5402:Pcdhga3'
ID |
430080 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Pcdhga3
|
Ensembl Gene |
ENSMUSG00000104346 |
Gene Name |
protocadherin gamma subfamily A, 3 |
Synonyms |
|
MMRRC Submission |
042973-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.121)
|
Stock # |
R5402 (G1)
|
Quality Score |
225 |
Status
|
Not validated
|
Chromosome |
18 |
Chromosomal Location |
37807388-37974926 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
G to A
at 37808747 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Arginine to Glutamine
at position 400
(R400Q)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000073150
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000073447]
[ENSMUST00000115661]
[ENSMUST00000192931]
[ENSMUST00000193869]
[ENSMUST00000194190]
[ENSMUST00000194544]
|
AlphaFold |
Q91XY5 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000073447
AA Change: R400Q
PolyPhen 2
Score 0.334 (Sensitivity: 0.90; Specificity: 0.89)
|
SMART Domains |
Protein: ENSMUSP00000073150 Gene: ENSMUSG00000104346 AA Change: R400Q
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
22 |
N/A |
INTRINSIC |
CA
|
42 |
128 |
2.15e-2 |
SMART |
CA
|
152 |
237 |
4.8e-13 |
SMART |
CA
|
261 |
342 |
9.36e-25 |
SMART |
CA
|
366 |
447 |
6.62e-25 |
SMART |
CA
|
471 |
557 |
6.72e-26 |
SMART |
CA
|
588 |
666 |
2.15e-15 |
SMART |
Pfam:Cadherin_C_2
|
685 |
768 |
4.8e-24 |
PFAM |
Pfam:Cadherin_tail
|
805 |
928 |
8.1e-38 |
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: ENSMUST00000192931
|
SMART Domains |
Protein: ENSMUSP00000141348 Gene: ENSMUSG00000103037
Domain | Start | End | E-Value | Type |
CA
|
36 |
119 |
8e-3 |
SMART |
CA
|
143 |
228 |
1.34e-20 |
SMART |
CA
|
252 |
333 |
1.52e-24 |
SMART |
CA
|
357 |
438 |
9.22e-24 |
SMART |
CA
|
462 |
548 |
1.24e-24 |
SMART |
CA
|
579 |
660 |
1.3e-9 |
SMART |
transmembrane domain
|
679 |
701 |
N/A |
INTRINSIC |
low complexity region
|
899 |
918 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000193869
|
SMART Domains |
Protein: ENSMUSP00000141482 Gene: ENSMUSG00000103332
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
28 |
N/A |
INTRINSIC |
CA
|
45 |
131 |
1.64e-2 |
SMART |
CA
|
155 |
240 |
6.42e-23 |
SMART |
CA
|
264 |
345 |
1.76e-20 |
SMART |
CA
|
369 |
450 |
2.27e-23 |
SMART |
CA
|
474 |
560 |
1.5e-23 |
SMART |
CA
|
591 |
669 |
1.17e-16 |
SMART |
transmembrane domain
|
692 |
714 |
N/A |
INTRINSIC |
low complexity region
|
912 |
931 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000193984
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000194190
|
SMART Domains |
Protein: ENSMUSP00000142062 Gene: ENSMUSG00000103144
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
28 |
N/A |
INTRINSIC |
CA
|
31 |
131 |
3.16e-2 |
SMART |
CA
|
155 |
240 |
5.39e-16 |
SMART |
CA
|
264 |
345 |
6.72e-26 |
SMART |
CA
|
369 |
450 |
1.32e-24 |
SMART |
CA
|
474 |
560 |
4.17e-22 |
SMART |
CA
|
591 |
669 |
4.48e-13 |
SMART |
transmembrane domain
|
692 |
714 |
N/A |
INTRINSIC |
low complexity region
|
912 |
931 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000194544
|
SMART Domains |
Protein: ENSMUSP00000141847 Gene: ENSMUSG00000102836
Domain | Start | End | E-Value | Type |
Blast:CA
|
18 |
66 |
5e-20 |
BLAST |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000195624
|
Coding Region Coverage |
- 1x: 99.4%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.7%
|
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 gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 49 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adgrv1 |
A |
T |
13: 81,607,834 (GRCm39) |
D4079E |
probably benign |
Het |
Bcar1 |
T |
C |
8: 112,440,962 (GRCm39) |
D344G |
probably damaging |
Het |
Car9 |
A |
G |
4: 43,510,213 (GRCm39) |
N265S |
probably damaging |
Het |
Ccr7 |
A |
G |
11: 99,036,560 (GRCm39) |
S121P |
possibly damaging |
Het |
Cgnl1 |
A |
G |
9: 71,536,603 (GRCm39) |
L1278P |
probably damaging |
Het |
Chst9 |
A |
T |
18: 15,585,872 (GRCm39) |
S230R |
probably damaging |
Het |
Cped1 |
G |
A |
6: 22,143,951 (GRCm39) |
V566M |
probably benign |
Het |
Csf2 |
A |
T |
11: 54,138,489 (GRCm39) |
Y117* |
probably null |
Het |
Cwf19l1 |
C |
T |
19: 44,121,524 (GRCm39) |
|
probably null |
Het |
Cyp2d34 |
C |
T |
15: 82,503,287 (GRCm39) |
G69D |
probably damaging |
Het |
Dync2h1 |
A |
T |
9: 7,114,949 (GRCm39) |
V170E |
probably damaging |
Het |
Ehbp1l1 |
T |
A |
19: 5,766,348 (GRCm39) |
T388S |
possibly damaging |
Het |
Etfa |
T |
C |
9: 55,362,023 (GRCm39) |
I329M |
probably benign |
Het |
Flt4 |
AC |
ACC |
11: 49,541,861 (GRCm39) |
|
probably null |
Het |
Fmnl2 |
G |
A |
2: 53,018,794 (GRCm39) |
V1078I |
probably damaging |
Het |
Fnip2 |
A |
G |
3: 79,388,250 (GRCm39) |
L797P |
possibly damaging |
Het |
Gmeb2 |
A |
T |
2: 180,897,750 (GRCm39) |
|
probably null |
Het |
Greb1l |
A |
G |
18: 10,537,169 (GRCm39) |
T1045A |
probably benign |
Het |
Hapln1 |
A |
G |
13: 89,753,530 (GRCm39) |
N232S |
probably benign |
Het |
Hibadh |
A |
T |
6: 52,523,965 (GRCm39) |
M311K |
probably benign |
Het |
Hus1 |
C |
T |
11: 8,960,240 (GRCm39) |
|
probably null |
Het |
Il31ra |
T |
C |
13: 112,660,669 (GRCm39) |
E640G |
probably benign |
Het |
L3mbtl4 |
T |
C |
17: 68,762,769 (GRCm39) |
F101L |
probably damaging |
Het |
Lbr |
A |
T |
1: 181,647,526 (GRCm39) |
M417K |
probably benign |
Het |
Lrig3 |
T |
G |
10: 125,844,609 (GRCm39) |
L691R |
probably damaging |
Het |
Mcm3ap |
T |
A |
10: 76,319,148 (GRCm39) |
F792Y |
probably benign |
Het |
Mst1 |
T |
C |
9: 107,961,408 (GRCm39) |
|
probably null |
Het |
Nova2 |
C |
A |
7: 18,692,371 (GRCm39) |
T500K |
probably damaging |
Het |
Nxph4 |
A |
T |
10: 127,362,133 (GRCm39) |
C253S |
probably damaging |
Het |
Or2t1 |
T |
C |
14: 14,328,878 (GRCm38) |
Y256H |
probably damaging |
Het |
Or4s2b |
T |
A |
2: 88,508,492 (GRCm39) |
S98T |
possibly damaging |
Het |
Pidd1 |
C |
A |
7: 141,018,507 (GRCm39) |
A915S |
probably damaging |
Het |
Plat |
T |
G |
8: 23,262,738 (GRCm39) |
W148G |
probably damaging |
Het |
Polr3a |
T |
C |
14: 24,505,009 (GRCm39) |
I1084V |
possibly damaging |
Het |
Pramel27 |
G |
A |
4: 143,578,225 (GRCm39) |
|
probably null |
Het |
Ptdss1 |
A |
G |
13: 67,081,663 (GRCm39) |
D31G |
possibly damaging |
Het |
Rnd2 |
C |
T |
11: 101,359,825 (GRCm39) |
L57F |
probably damaging |
Het |
Samd8 |
A |
G |
14: 21,825,236 (GRCm39) |
D64G |
probably damaging |
Het |
Scgb1b20 |
A |
G |
7: 33,072,656 (GRCm39) |
|
probably null |
Het |
Sh3bp5 |
C |
A |
14: 31,099,452 (GRCm39) |
R265L |
probably benign |
Het |
Slc25a23 |
T |
C |
17: 57,360,336 (GRCm39) |
I269V |
probably benign |
Het |
Slc35f4 |
A |
T |
14: 49,556,331 (GRCm39) |
S141T |
probably damaging |
Het |
Srgap1 |
T |
C |
10: 121,621,665 (GRCm39) |
M966V |
probably benign |
Het |
Syne2 |
T |
A |
12: 76,106,213 (GRCm39) |
V5526E |
probably damaging |
Het |
Tcaf3 |
A |
G |
6: 42,568,860 (GRCm39) |
S596P |
probably benign |
Het |
Tg |
T |
A |
15: 66,611,017 (GRCm39) |
I356N |
probably damaging |
Het |
Ttc6 |
C |
T |
12: 57,783,817 (GRCm39) |
R1759* |
probably null |
Het |
Wdsub1 |
T |
C |
2: 59,700,822 (GRCm39) |
N138D |
probably benign |
Het |
Zfp1001 |
A |
G |
2: 150,204,886 (GRCm39) |
I67V |
probably benign |
Het |
|
Other mutations in Pcdhga3 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL00934:Pcdhga3
|
APN |
18 |
37,808,486 (GRCm39) |
missense |
possibly damaging |
0.92 |
R2863:Pcdhga3
|
UTSW |
18 |
37,807,643 (GRCm39) |
missense |
probably damaging |
0.99 |
R4446:Pcdhga3
|
UTSW |
18 |
37,808,938 (GRCm39) |
missense |
probably damaging |
0.99 |
R4581:Pcdhga3
|
UTSW |
18 |
37,809,934 (GRCm39) |
missense |
probably benign |
0.00 |
R4747:Pcdhga3
|
UTSW |
18 |
37,809,799 (GRCm39) |
missense |
probably benign |
0.29 |
R4964:Pcdhga3
|
UTSW |
18 |
37,809,154 (GRCm39) |
missense |
probably benign |
0.05 |
R5165:Pcdhga3
|
UTSW |
18 |
37,808,723 (GRCm39) |
missense |
possibly damaging |
0.60 |
R5210:Pcdhga3
|
UTSW |
18 |
37,808,963 (GRCm39) |
missense |
probably benign |
0.03 |
R5370:Pcdhga3
|
UTSW |
18 |
37,808,343 (GRCm39) |
missense |
probably damaging |
1.00 |
R5610:Pcdhga3
|
UTSW |
18 |
37,808,276 (GRCm39) |
missense |
possibly damaging |
0.83 |
R5782:Pcdhga3
|
UTSW |
18 |
37,809,353 (GRCm39) |
missense |
possibly damaging |
0.91 |
R5889:Pcdhga3
|
UTSW |
18 |
37,809,662 (GRCm39) |
missense |
probably damaging |
1.00 |
R6058:Pcdhga3
|
UTSW |
18 |
37,808,141 (GRCm39) |
missense |
probably damaging |
1.00 |
R6127:Pcdhga3
|
UTSW |
18 |
37,807,757 (GRCm39) |
missense |
probably damaging |
0.98 |
R6307:Pcdhga3
|
UTSW |
18 |
37,809,674 (GRCm39) |
unclassified |
probably benign |
|
R6893:Pcdhga3
|
UTSW |
18 |
37,809,598 (GRCm39) |
missense |
probably benign |
0.37 |
R7013:Pcdhga3
|
UTSW |
18 |
37,808,674 (GRCm39) |
missense |
probably damaging |
1.00 |
R7174:Pcdhga3
|
UTSW |
18 |
37,808,980 (GRCm39) |
missense |
probably benign |
0.02 |
R7448:Pcdhga3
|
UTSW |
18 |
37,808,917 (GRCm39) |
missense |
possibly damaging |
0.94 |
R7492:Pcdhga3
|
UTSW |
18 |
37,809,178 (GRCm39) |
missense |
probably benign |
0.01 |
R7509:Pcdhga3
|
UTSW |
18 |
37,808,910 (GRCm39) |
nonsense |
probably null |
|
R7914:Pcdhga3
|
UTSW |
18 |
37,808,013 (GRCm39) |
missense |
probably benign |
0.00 |
R7984:Pcdhga3
|
UTSW |
18 |
37,809,549 (GRCm39) |
missense |
probably benign |
0.00 |
R8782:Pcdhga3
|
UTSW |
18 |
37,807,865 (GRCm39) |
missense |
probably damaging |
1.00 |
R9157:Pcdhga3
|
UTSW |
18 |
37,809,229 (GRCm39) |
missense |
probably benign |
0.40 |
R9169:Pcdhga3
|
UTSW |
18 |
37,809,088 (GRCm39) |
missense |
probably damaging |
1.00 |
R9436:Pcdhga3
|
UTSW |
18 |
37,808,144 (GRCm39) |
missense |
probably damaging |
1.00 |
R9437:Pcdhga3
|
UTSW |
18 |
37,808,144 (GRCm39) |
missense |
probably damaging |
1.00 |
R9588:Pcdhga3
|
UTSW |
18 |
37,808,564 (GRCm39) |
missense |
probably damaging |
1.00 |
R9767:Pcdhga3
|
UTSW |
18 |
37,808,096 (GRCm39) |
missense |
probably benign |
0.00 |
R9778:Pcdhga3
|
UTSW |
18 |
37,807,786 (GRCm39) |
missense |
probably benign |
0.42 |
Z1177:Pcdhga3
|
UTSW |
18 |
37,809,674 (GRCm39) |
unclassified |
probably benign |
|
|
Predicted Primers |
PCR Primer
(F):5'- ATGTGAATGACAACGCCCCG -3'
(R):5'- TCTGGGTCCTGTGCTGTAAC -3'
Sequencing Primer
(F):5'- CCGGAAGTCTCAGTCACTTC -3'
(R):5'- AAGATGGAGGCTCCCCTAG -3'
|
Posted On |
2016-09-06 |