Incidental Mutation 'R4165:Pcdhb19'
| ID |
321713 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pcdhb19
|
| Ensembl Gene |
ENSMUSG00000043313 |
| Gene Name |
protocadherin beta 19 |
| Synonyms |
Pcdhb11, PcdhbS |
| MMRRC Submission |
041007-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.054)
|
| Stock # |
R4165 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
18 |
| Chromosomal Location |
37630049-37637181 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 37632243 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Lysine
at position 679
(N679K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000053326
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000055949]
[ENSMUST00000059571]
[ENSMUST00000115661]
[ENSMUST00000194544]
|
| AlphaFold |
Q91Y01 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000055949
|
| SMART Domains |
Protein: ENSMUSP00000052113
Gene: ENSMUSG00000048347
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
26 |
N/A |
INTRINSIC |
|
Pfam:Cadherin_2
|
30 |
112 |
3.1e-34 |
PFAM |
|
CA
|
155 |
240 |
7.97e-19 |
SMART |
|
CA
|
264 |
345 |
6.27e-26 |
SMART |
|
CA
|
368 |
449 |
2.63e-19 |
SMART |
|
CA
|
473 |
559 |
7.09e-25 |
SMART |
|
CA
|
589 |
670 |
2.87e-11 |
SMART |
|
Pfam:Cadherin_C_2
|
687 |
771 |
7.9e-27 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000059571
AA Change: N679K
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000053326
Gene: ENSMUSG00000043313
AA Change: N679K
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
26 |
N/A |
INTRINSIC |
|
CA
|
45 |
131 |
4.8e-1 |
SMART |
|
CA
|
155 |
240 |
6.58e-20 |
SMART |
|
CA
|
264 |
345 |
1.03e-21 |
SMART |
|
CA
|
368 |
449 |
4.21e-18 |
SMART |
|
CA
|
473 |
559 |
3.36e-26 |
SMART |
|
CA
|
589 |
670 |
6.69e-12 |
SMART |
|
Pfam:Cadherin_C_2
|
686 |
769 |
1.9e-25 |
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: ENSMUST00000193984
|
| 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 |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.8%
- 10x: 97.6%
- 20x: 96.1%
|
| Validation Efficiency |
97% (38/39) |
| 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 beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 38 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aak1 |
T |
A |
6: 86,827,044 (GRCm39) |
F4I |
probably damaging |
Het |
| Adamts8 |
G |
T |
9: 30,862,684 (GRCm39) |
E296D |
probably benign |
Het |
| Alg11 |
T |
C |
8: 22,555,573 (GRCm39) |
V278A |
probably damaging |
Het |
| Ankfy1 |
G |
A |
11: 72,605,310 (GRCm39) |
|
probably null |
Het |
| Avil |
C |
T |
10: 126,842,496 (GRCm39) |
Q92* |
probably null |
Het |
| Cfap300 |
A |
T |
9: 8,026,071 (GRCm39) |
L167Q |
probably damaging |
Het |
| CK137956 |
A |
T |
4: 127,864,522 (GRCm39) |
S36T |
possibly damaging |
Het |
| Epb41l3 |
T |
C |
17: 69,514,883 (GRCm39) |
S7P |
probably damaging |
Het |
| Espl1 |
A |
G |
15: 102,221,424 (GRCm39) |
I944V |
probably damaging |
Het |
| Fsd2 |
T |
C |
7: 81,195,608 (GRCm39) |
T434A |
probably damaging |
Het |
| Gm5174 |
A |
G |
10: 86,492,797 (GRCm39) |
|
noncoding transcript |
Het |
| Gpaa1 |
A |
C |
15: 76,216,667 (GRCm39) |
|
probably benign |
Het |
| Grina |
T |
A |
15: 76,133,529 (GRCm39) |
L334Q |
probably damaging |
Het |
| Gvin-ps5 |
T |
A |
7: 105,929,895 (GRCm39) |
|
noncoding transcript |
Het |
| Igkv15-103 |
G |
T |
6: 68,414,824 (GRCm39) |
G88* |
probably null |
Het |
| Ip6k2 |
G |
A |
9: 108,682,847 (GRCm39) |
R319Q |
probably benign |
Het |
| Kdm3b |
A |
T |
18: 34,928,797 (GRCm39) |
I183F |
probably benign |
Het |
| Kyat3 |
A |
G |
3: 142,432,066 (GRCm39) |
|
probably null |
Het |
| Larp7 |
A |
G |
3: 127,330,611 (GRCm39) |
Y569H |
probably benign |
Het |
| Loxhd1 |
A |
T |
18: 77,460,025 (GRCm39) |
I758F |
probably damaging |
Het |
| Nr1d2 |
T |
C |
14: 18,215,446 (GRCm38) |
I189V |
probably benign |
Het |
| Odad2 |
A |
T |
18: 7,217,008 (GRCm39) |
I668K |
probably damaging |
Het |
| Pigr |
G |
A |
1: 130,769,554 (GRCm39) |
D122N |
probably benign |
Het |
| Prap1 |
T |
A |
7: 139,676,091 (GRCm39) |
V35E |
probably benign |
Het |
| Prdm1 |
T |
A |
10: 44,317,572 (GRCm39) |
Y417F |
probably benign |
Het |
| Ralgapa1 |
C |
T |
12: 55,687,429 (GRCm39) |
R2019Q |
probably damaging |
Het |
| Rps3 |
T |
C |
7: 99,132,816 (GRCm39) |
I5V |
probably benign |
Het |
| Sema3a |
A |
T |
5: 13,523,364 (GRCm39) |
|
probably null |
Het |
| Serpina3g |
A |
T |
12: 104,206,546 (GRCm39) |
T116S |
probably benign |
Het |
| Skint11 |
C |
A |
4: 114,101,856 (GRCm39) |
Q99K |
probably benign |
Het |
| Slc22a28 |
A |
G |
19: 8,040,773 (GRCm39) |
S493P |
possibly damaging |
Het |
| Snapc1 |
G |
T |
12: 74,029,354 (GRCm39) |
|
probably null |
Het |
| Sobp |
C |
T |
10: 42,897,644 (GRCm39) |
G647D |
probably damaging |
Het |
| Tomm22 |
C |
A |
15: 79,555,206 (GRCm39) |
|
probably benign |
Het |
| Trappc11 |
T |
C |
8: 47,978,003 (GRCm39) |
|
probably benign |
Het |
| Txnl4a |
T |
A |
18: 80,265,471 (GRCm39) |
M112K |
probably benign |
Het |
| Vmn2r16 |
T |
C |
5: 109,478,427 (GRCm39) |
F61L |
possibly damaging |
Het |
| Zfp709 |
C |
T |
8: 72,644,649 (GRCm39) |
Q693* |
probably null |
Het |
|
| Other mutations in Pcdhb19 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01374:Pcdhb19
|
APN |
18 |
37,631,042 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02070:Pcdhb19
|
APN |
18 |
37,631,597 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02348:Pcdhb19
|
APN |
18 |
37,631,861 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02866:Pcdhb19
|
APN |
18 |
37,632,163 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
IGL02869:Pcdhb19
|
APN |
18 |
37,631,690 (GRCm39) |
missense |
probably damaging |
0.98 |
|
IGL03118:Pcdhb19
|
APN |
18 |
37,632,618 (GRCm39) |
intron |
probably benign |
|
|
IGL03120:Pcdhb19
|
APN |
18 |
37,631,209 (GRCm39) |
missense |
probably benign |
0.09 |
|
IGL03135:Pcdhb19
|
APN |
18 |
37,631,588 (GRCm39) |
missense |
probably benign |
0.37 |
|
IGL03366:Pcdhb19
|
APN |
18 |
37,631,665 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R0147:Pcdhb19
|
UTSW |
18 |
37,630,235 (GRCm39) |
missense |
probably benign |
0.01 |
|
R0148:Pcdhb19
|
UTSW |
18 |
37,630,235 (GRCm39) |
missense |
probably benign |
0.01 |
|
R0432:Pcdhb19
|
UTSW |
18 |
37,632,588 (GRCm39) |
missense |
probably benign |
0.01 |
|
R0609:Pcdhb19
|
UTSW |
18 |
37,631,005 (GRCm39) |
missense |
probably benign |
|
|
R1438:Pcdhb19
|
UTSW |
18 |
37,631,015 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2255:Pcdhb19
|
UTSW |
18 |
37,630,997 (GRCm39) |
missense |
probably benign |
0.00 |
|
R2265:Pcdhb19
|
UTSW |
18 |
37,630,736 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R3500:Pcdhb19
|
UTSW |
18 |
37,630,532 (GRCm39) |
nonsense |
probably null |
|
|
R3708:Pcdhb19
|
UTSW |
18 |
37,630,442 (GRCm39) |
missense |
probably benign |
0.04 |
|
R4166:Pcdhb19
|
UTSW |
18 |
37,632,243 (GRCm39) |
missense |
probably benign |
|
|
R4863:Pcdhb19
|
UTSW |
18 |
37,632,161 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5217:Pcdhb19
|
UTSW |
18 |
37,630,939 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5770:Pcdhb19
|
UTSW |
18 |
37,631,090 (GRCm39) |
missense |
possibly damaging |
0.73 |
|
R6031:Pcdhb19
|
UTSW |
18 |
37,630,776 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6031:Pcdhb19
|
UTSW |
18 |
37,630,776 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6372:Pcdhb19
|
UTSW |
18 |
37,630,419 (GRCm39) |
missense |
probably benign |
0.04 |
|
R6454:Pcdhb19
|
UTSW |
18 |
37,632,322 (GRCm39) |
missense |
probably benign |
0.43 |
|
R6985:Pcdhb19
|
UTSW |
18 |
37,630,211 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7658:Pcdhb19
|
UTSW |
18 |
37,632,034 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7662:Pcdhb19
|
UTSW |
18 |
37,631,788 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R7910:Pcdhb19
|
UTSW |
18 |
37,630,720 (GRCm39) |
missense |
probably benign |
0.43 |
|
R8041:Pcdhb19
|
UTSW |
18 |
37,630,367 (GRCm39) |
missense |
possibly damaging |
0.87 |
|
R8318:Pcdhb19
|
UTSW |
18 |
37,630,999 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R8989:Pcdhb19
|
UTSW |
18 |
37,631,476 (GRCm39) |
missense |
probably benign |
0.04 |
|
R9053:Pcdhb19
|
UTSW |
18 |
37,631,143 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9164:Pcdhb19
|
UTSW |
18 |
37,631,852 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9197:Pcdhb19
|
UTSW |
18 |
37,631,354 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9309:Pcdhb19
|
UTSW |
18 |
37,631,858 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9377:Pcdhb19
|
UTSW |
18 |
37,632,299 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9402:Pcdhb19
|
UTSW |
18 |
37,632,532 (GRCm39) |
nonsense |
probably null |
|
|
R9432:Pcdhb19
|
UTSW |
18 |
37,630,628 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R9553:Pcdhb19
|
UTSW |
18 |
37,631,848 (GRCm39) |
missense |
probably damaging |
1.00 |
|
X0062:Pcdhb19
|
UTSW |
18 |
37,630,228 (GRCm39) |
missense |
probably benign |
|
|
Z1177:Pcdhb19
|
UTSW |
18 |
37,631,498 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TTCCAGCTGCTCAAGGCTAC -3'
(R):5'- CCATGAGATGGTCAGGAAAGTGTC -3'
Sequencing Primer
(F):5'- CACACAATGGCGAGGTGC -3'
(R):5'- GAAAGTGTCCCTCAGGCACAG -3'
|
| Posted On |
2015-06-12 |
Incidental Mutation