Incidental Mutation 'R9292:Pcdhga4'
| ID |
704362 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdhga4
|
| Ensembl Gene |
ENSMUSG00000103677 |
| Gene Name |
protocadherin gamma subfamily A, 4 |
| Synonyms |
|
| MMRRC Submission |
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.132)
|
| Stock # |
R9292 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
37818290-37974923 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 37819713 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Leucine
at position 421
(I421L)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000142140
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000073447]
[ENSMUST00000115661]
[ENSMUST00000192931]
[ENSMUST00000193869]
[ENSMUST00000194190]
[ENSMUST00000194418]
[ENSMUST00000194544]
[ENSMUST00000195112]
|
| AlphaFold |
Q91XY4 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000073447
|
| SMART Domains |
Protein: ENSMUSP00000073150
Gene: ENSMUSG00000104346
| 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: ENSMUST00000194418
AA Change: I421L
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
| SMART Domains |
Protein: ENSMUSP00000142140
Gene: ENSMUSG00000103677
AA Change: I421L
| Domain | Start | End | E-Value | Type |
|---|
|
CA
|
44 |
130 |
1.64e-2 |
SMART |
|
CA
|
154 |
239 |
3.93e-18 |
SMART |
|
CA
|
263 |
344 |
5.22e-23 |
SMART |
|
CA
|
368 |
449 |
5.02e-25 |
SMART |
|
CA
|
473 |
559 |
2.07e-26 |
SMART |
|
CA
|
590 |
668 |
6.84e-18 |
SMART |
|
transmembrane domain
|
690 |
712 |
N/A |
INTRINSIC |
|
low complexity region
|
911 |
930 |
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 |
probably benign
Transcript: ENSMUST00000195112
|
| SMART Domains |
Protein: ENSMUSP00000141449
Gene: ENSMUSG00000102748
| Domain | Start | End | E-Value | Type |
|---|
|
CA
|
24 |
130 |
8.18e-3 |
SMART |
|
CA
|
154 |
239 |
1.39e-18 |
SMART |
|
CA
|
263 |
344 |
7.91e-23 |
SMART |
|
CA
|
368 |
449 |
2.27e-23 |
SMART |
|
CA
|
473 |
559 |
1.24e-24 |
SMART |
|
CA
|
590 |
671 |
1.3e-9 |
SMART |
|
transmembrane domain
|
690 |
712 |
N/A |
INTRINSIC |
|
low complexity region
|
909 |
928 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000195163
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.5%
|
| Validation Efficiency |
100% (58/58) |
| 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: 59 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb1b |
C |
T |
5: 8,862,843 (GRCm39) |
T175I |
probably benign |
Het |
| Acat3 |
T |
C |
17: 13,146,255 (GRCm39) |
T243A |
probably benign |
Het |
| Aebp1 |
C |
A |
11: 5,815,260 (GRCm39) |
P264Q |
possibly damaging |
Het |
| Aldh1l1 |
T |
C |
6: 90,568,867 (GRCm39) |
F723L |
probably damaging |
Het |
| Atp13a4 |
T |
A |
16: 29,241,500 (GRCm39) |
I723F |
|
Het |
| Bop1 |
T |
C |
15: 76,351,031 (GRCm39) |
T97A |
probably benign |
Het |
| Casq1 |
T |
C |
1: 172,043,114 (GRCm39) |
Y194C |
probably damaging |
Het |
| Cep250 |
G |
A |
2: 155,832,688 (GRCm39) |
E1538K |
probably damaging |
Het |
| Col12a1 |
A |
T |
9: 79,585,805 (GRCm39) |
V1218E |
probably benign |
Het |
| Coq10b |
T |
A |
1: 55,110,868 (GRCm39) |
M212K |
probably damaging |
Het |
| Dchs1 |
T |
C |
7: 105,403,120 (GRCm39) |
T3141A |
probably damaging |
Het |
| Dnajc10 |
A |
G |
2: 80,176,916 (GRCm39) |
T624A |
probably benign |
Het |
| Dock8 |
A |
G |
19: 25,160,995 (GRCm39) |
|
probably benign |
Het |
| Dsg1c |
T |
A |
18: 20,416,775 (GRCm39) |
V892E |
probably damaging |
Het |
| Eif4g3 |
A |
G |
4: 137,921,382 (GRCm39) |
R1370G |
possibly damaging |
Het |
| Elmo1 |
T |
G |
13: 20,784,429 (GRCm39) |
|
probably null |
Het |
| Erc2 |
T |
A |
14: 27,498,799 (GRCm39) |
I225N |
probably damaging |
Het |
| Ermp1 |
C |
A |
19: 29,606,049 (GRCm39) |
V422L |
probably benign |
Het |
| Fam124b |
T |
A |
1: 80,191,221 (GRCm39) |
H54L |
probably benign |
Het |
| Gabbr1 |
T |
G |
17: 37,366,784 (GRCm39) |
I336S |
possibly damaging |
Het |
| Galk2 |
T |
C |
2: 125,817,218 (GRCm39) |
Y336H |
probably damaging |
Het |
| Gm40460 |
CACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAG |
CACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAG |
7: 141,794,554 (GRCm39) |
|
probably benign |
Het |
| Grm4 |
A |
G |
17: 27,692,037 (GRCm39) |
F194S |
probably damaging |
Het |
| Gtf2a1 |
G |
A |
12: 91,534,964 (GRCm39) |
Q189* |
probably null |
Het |
| Gtf3c1 |
T |
C |
7: 125,273,563 (GRCm39) |
|
probably benign |
Het |
| Hspa2 |
A |
G |
12: 76,452,047 (GRCm39) |
E247G |
probably damaging |
Het |
| Lpar1 |
T |
C |
4: 58,486,558 (GRCm39) |
R238G |
probably benign |
Het |
| Ltbp1 |
C |
A |
17: 75,583,436 (GRCm39) |
S412Y |
probably damaging |
Het |
| Nup210 |
A |
C |
6: 91,051,235 (GRCm39) |
S383A |
possibly damaging |
Het |
| Or10j3 |
C |
T |
1: 173,031,099 (GRCm39) |
P59S |
probably damaging |
Het |
| Or11g2 |
T |
C |
14: 50,856,513 (GRCm39) |
V278A |
possibly damaging |
Het |
| Or8b51 |
T |
A |
9: 38,569,071 (GRCm39) |
N206Y |
probably damaging |
Het |
| Pah |
T |
A |
10: 87,403,218 (GRCm39) |
Y198N |
probably damaging |
Het |
| Pde6b |
T |
C |
5: 108,536,751 (GRCm39) |
I149T |
probably benign |
Het |
| Peli3 |
G |
A |
19: 4,988,117 (GRCm39) |
P81L |
possibly damaging |
Het |
| Pfdn5 |
T |
C |
15: 102,234,883 (GRCm39) |
S30P |
possibly damaging |
Het |
| Plcb3 |
A |
T |
19: 6,942,042 (GRCm39) |
L263Q |
probably damaging |
Het |
| Pld3 |
T |
C |
7: 27,238,879 (GRCm39) |
M190V |
probably benign |
Het |
| Rab6a |
A |
G |
7: 100,285,963 (GRCm39) |
E186G |
probably benign |
Het |
| Ralyl |
T |
A |
3: 14,172,312 (GRCm39) |
D60E |
probably benign |
Het |
| Rtl1 |
G |
A |
12: 109,556,673 (GRCm39) |
A1722V |
possibly damaging |
Het |
| Scarf1 |
T |
C |
11: 75,406,006 (GRCm39) |
Y97H |
probably damaging |
Het |
| Sf3a2 |
T |
A |
10: 80,640,560 (GRCm39) |
V457E |
unknown |
Het |
| Sh2d4b |
C |
G |
14: 40,537,914 (GRCm39) |
E403Q |
probably damaging |
Het |
| Slc12a7 |
A |
G |
13: 73,932,707 (GRCm39) |
E65G |
possibly damaging |
Het |
| Spink5 |
T |
C |
18: 44,148,075 (GRCm39) |
V905A |
possibly damaging |
Het |
| Spred1 |
T |
C |
2: 117,005,832 (GRCm39) |
F198S |
probably benign |
Het |
| St18 |
C |
A |
1: 6,898,106 (GRCm39) |
T636K |
probably benign |
Het |
| Stag3 |
T |
A |
5: 138,299,712 (GRCm39) |
D874E |
probably benign |
Het |
| Suco |
T |
C |
1: 161,671,574 (GRCm39) |
T502A |
probably damaging |
Het |
| Swt1 |
T |
C |
1: 151,278,787 (GRCm39) |
I457V |
probably benign |
Het |
| Syne2 |
G |
T |
12: 75,997,823 (GRCm39) |
C2266F |
probably benign |
Het |
| Tcirg1 |
T |
C |
19: 3,947,840 (GRCm39) |
N532D |
probably damaging |
Het |
| Tfdp1 |
T |
A |
8: 13,420,580 (GRCm39) |
N136K |
probably benign |
Het |
| Tmem245 |
T |
C |
4: 56,926,173 (GRCm39) |
|
probably benign |
Het |
| Tmem245 |
T |
C |
4: 56,937,979 (GRCm39) |
I190V |
probably benign |
Het |
| Trp53bp1 |
C |
T |
2: 121,046,177 (GRCm39) |
V1208M |
probably damaging |
Het |
| Tulp1 |
T |
A |
17: 28,582,738 (GRCm39) |
K137* |
probably null |
Het |
| Zfp534 |
A |
T |
4: 147,759,095 (GRCm39) |
C525S |
probably damaging |
Het |
|
| Other mutations in Pcdhga4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
PIT1430001:Pcdhga4
|
UTSW |
18 |
37,819,267 (GRCm39) |
missense |
probably benign |
0.00 |
|
R3828:Pcdhga4
|
UTSW |
18 |
37,820,654 (GRCm39) |
missense |
possibly damaging |
0.62 |
|
R3970:Pcdhga4
|
UTSW |
18 |
37,820,654 (GRCm39) |
missense |
possibly damaging |
0.62 |
|
R4080:Pcdhga4
|
UTSW |
18 |
37,818,832 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4356:Pcdhga4
|
UTSW |
18 |
37,820,664 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4834:Pcdhga4
|
UTSW |
18 |
37,818,490 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4983:Pcdhga4
|
UTSW |
18 |
37,819,572 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5076:Pcdhga4
|
UTSW |
18 |
37,818,648 (GRCm39) |
missense |
probably benign |
0.43 |
|
R5186:Pcdhga4
|
UTSW |
18 |
37,820,479 (GRCm39) |
missense |
probably benign |
0.07 |
|
R5194:Pcdhga4
|
UTSW |
18 |
37,820,794 (GRCm39) |
missense |
probably benign |
0.08 |
|
R5326:Pcdhga4
|
UTSW |
18 |
37,819,651 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5333:Pcdhga4
|
UTSW |
18 |
37,818,477 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5373:Pcdhga4
|
UTSW |
18 |
37,818,649 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5374:Pcdhga4
|
UTSW |
18 |
37,818,649 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5419:Pcdhga4
|
UTSW |
18 |
37,819,798 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5542:Pcdhga4
|
UTSW |
18 |
37,819,651 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R5878:Pcdhga4
|
UTSW |
18 |
37,820,739 (GRCm39) |
missense |
probably benign |
0.03 |
|
R5996:Pcdhga4
|
UTSW |
18 |
37,818,991 (GRCm39) |
missense |
probably benign |
0.03 |
|
R6056:Pcdhga4
|
UTSW |
18 |
37,819,383 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6083:Pcdhga4
|
UTSW |
18 |
37,820,478 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R6155:Pcdhga4
|
UTSW |
18 |
37,819,546 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R6208:Pcdhga4
|
UTSW |
18 |
37,819,762 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6306:Pcdhga4
|
UTSW |
18 |
37,818,966 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6580:Pcdhga4
|
UTSW |
18 |
37,820,370 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R6936:Pcdhga4
|
UTSW |
18 |
37,820,458 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
R7132:Pcdhga4
|
UTSW |
18 |
37,820,430 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7159:Pcdhga4
|
UTSW |
18 |
37,819,972 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7257:Pcdhga4
|
UTSW |
18 |
37,820,451 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7263:Pcdhga4
|
UTSW |
18 |
37,819,873 (GRCm39) |
missense |
probably benign |
0.42 |
|
R7825:Pcdhga4
|
UTSW |
18 |
37,820,374 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7882:Pcdhga4
|
UTSW |
18 |
37,819,681 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7916:Pcdhga4
|
UTSW |
18 |
37,818,502 (GRCm39) |
missense |
probably benign |
0.22 |
|
R8053:Pcdhga4
|
UTSW |
18 |
37,819,308 (GRCm39) |
missense |
probably benign |
0.07 |
|
R9184:Pcdhga4
|
UTSW |
18 |
37,820,460 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R9417:Pcdhga4
|
UTSW |
18 |
37,820,560 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9483:Pcdhga4
|
UTSW |
18 |
37,819,746 (GRCm39) |
missense |
possibly damaging |
0.73 |
|
R9562:Pcdhga4
|
UTSW |
18 |
37,819,527 (GRCm39) |
missense |
probably benign |
0.03 |
|
| Predicted Primers |
PCR Primer
(F):5'- CACCAGCTCTATCCAGGAAG -3'
(R):5'- GGCATTCTCACCACTGTCTG -3'
Sequencing Primer
(F):5'- TTCCCCAGGCACAGTGATTG -3'
(R):5'- ACCACTGTCTGGGTCCTG -3'
|
| Posted On |
2022-03-25 |
Incidental Mutation