Incidental Mutation 'R4125:Nectin4'
| ID |
315341 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Nectin4
|
| Ensembl Gene |
ENSMUSG00000006411 |
| Gene Name |
nectin cell adhesion molecule 4 |
| Synonyms |
Pvrl4, 1200017F15Rik, nectin 4, Prr4 |
| MMRRC Submission |
041633-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.079)
|
| Stock # |
R4125 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
171197741-171215855 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 171213301 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Glycine
at position 408
(S408G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000106917
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006578]
[ENSMUST00000056449]
[ENSMUST00000094325]
[ENSMUST00000111286]
|
| AlphaFold |
Q8R007 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000006578
AA Change: S408G
PolyPhen 2
Score 0.020 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000006578
Gene: ENSMUSG00000006411
AA Change: S408G
| Domain | Start | End | E-Value | Type |
|---|
|
IG
|
36 |
145 |
9.26e-8 |
SMART |
|
Pfam:Ig_2
|
147 |
241 |
4e-4 |
PFAM |
|
Pfam:C2-set_2
|
150 |
233 |
9e-17 |
PFAM |
|
IGc2
|
259 |
321 |
9.78e-7 |
SMART |
|
transmembrane domain
|
348 |
370 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000056449
|
| SMART Domains |
Protein: ENSMUSP00000059389
Gene: ENSMUSG00000048865
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
6 |
14 |
N/A |
INTRINSIC |
|
RhoGAP
|
31 |
212 |
1.4e-61 |
SMART |
|
Blast:RhoGAP
|
225 |
285 |
2e-24 |
BLAST |
|
low complexity region
|
348 |
366 |
N/A |
INTRINSIC |
|
low complexity region
|
367 |
378 |
N/A |
INTRINSIC |
|
low complexity region
|
452 |
463 |
N/A |
INTRINSIC |
|
low complexity region
|
498 |
510 |
N/A |
INTRINSIC |
|
low complexity region
|
514 |
534 |
N/A |
INTRINSIC |
|
low complexity region
|
667 |
690 |
N/A |
INTRINSIC |
|
low complexity region
|
736 |
752 |
N/A |
INTRINSIC |
|
low complexity region
|
924 |
940 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000094325
AA Change: S408G
PolyPhen 2
Score 0.020 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000091883
Gene: ENSMUSG00000006411
AA Change: S408G
| Domain | Start | End | E-Value | Type |
|---|
|
IG
|
36 |
145 |
9.26e-8 |
SMART |
|
Pfam:Ig_2
|
147 |
241 |
2.1e-4 |
PFAM |
|
Pfam:C2-set_2
|
150 |
233 |
8.7e-17 |
PFAM |
|
IGc2
|
259 |
321 |
9.78e-7 |
SMART |
|
transmembrane domain
|
348 |
370 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000111286
AA Change: S408G
PolyPhen 2
Score 0.020 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000106917
Gene: ENSMUSG00000006411
AA Change: S408G
| Domain | Start | End | E-Value | Type |
|---|
|
IG
|
100 |
209 |
9.26e-8 |
SMART |
|
Pfam:C2-set_2
|
214 |
297 |
1.2e-16 |
PFAM |
|
IGc2
|
323 |
385 |
9.78e-7 |
SMART |
|
transmembrane domain
|
412 |
434 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000131607
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000135312
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000194914
|
| Meta Mutation Damage Score |
0.0654 |
| Coding Region Coverage |
- 1x: 99.5%
- 3x: 98.7%
- 10x: 97.3%
- 20x: 95.1%
|
| Validation Efficiency |
98% (52/53) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the nectin family. The encoded protein contains two immunoglobulin-like (Ig-like) C2-type domains and one Ig-like V-type domain. It is involved in cell adhesion through trans-homophilic and -heterophilic interactions. It is a single-pass type I membrane protein. The soluble form is produced by proteolytic cleavage at the cell surface by the metalloproteinase ADAM17/TACE. The secreted form is found in both breast tumor cell lines and breast tumor patients. Mutations in this gene are the cause of ectodermal dysplasia-syndactyly syndrome type 1, an autosomal recessive disorder. Alternatively spliced transcript variants have been found but the full-length nature of the variant has not been determined.[provided by RefSeq, Jan 2011]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 49 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam30 |
T |
A |
3: 98,068,679 (GRCm39) |
C43S |
probably damaging |
Het |
| Adamts6 |
A |
T |
13: 104,449,412 (GRCm39) |
Y274F |
probably damaging |
Het |
| Ap2b1 |
A |
G |
11: 83,256,471 (GRCm39) |
|
probably null |
Het |
| Atm |
A |
C |
9: 53,361,921 (GRCm39) |
L2732R |
probably damaging |
Het |
| Bbox1 |
A |
G |
2: 110,100,525 (GRCm39) |
V224A |
probably benign |
Het |
| Bmpr1a |
T |
C |
14: 34,156,690 (GRCm39) |
D112G |
probably benign |
Het |
| Cdk19 |
A |
G |
10: 40,270,391 (GRCm39) |
I67V |
probably benign |
Het |
| Cds2 |
A |
G |
2: 132,139,191 (GRCm39) |
T145A |
probably benign |
Het |
| Chd9 |
A |
G |
8: 91,777,912 (GRCm39) |
D2641G |
probably damaging |
Het |
| Chn2 |
G |
T |
6: 54,249,963 (GRCm39) |
R24M |
probably damaging |
Het |
| Chuk |
T |
C |
19: 44,088,613 (GRCm39) |
I121V |
probably null |
Het |
| Ctsr |
A |
T |
13: 61,309,659 (GRCm39) |
D183E |
probably benign |
Het |
| Elp3 |
T |
C |
14: 65,797,630 (GRCm39) |
E347G |
possibly damaging |
Het |
| Fhip1a |
A |
G |
3: 85,572,690 (GRCm39) |
S988P |
possibly damaging |
Het |
| Gnas |
A |
G |
2: 174,141,958 (GRCm39) |
N709S |
possibly damaging |
Het |
| Gramd2b |
T |
C |
18: 56,618,296 (GRCm39) |
S199P |
probably damaging |
Het |
| Gtf3c1 |
A |
T |
7: 125,246,622 (GRCm39) |
C1562* |
probably null |
Het |
| Ifit1bl1 |
T |
A |
19: 34,572,188 (GRCm39) |
I90F |
probably damaging |
Het |
| Igf2r |
A |
T |
17: 12,921,141 (GRCm39) |
H1313Q |
possibly damaging |
Het |
| Ighj4 |
T |
C |
12: 113,392,176 (GRCm39) |
|
probably benign |
Het |
| Kansl2 |
G |
T |
15: 98,429,636 (GRCm39) |
P132Q |
possibly damaging |
Het |
| Lman1 |
T |
C |
18: 66,120,932 (GRCm39) |
H430R |
possibly damaging |
Het |
| Lrrk2 |
T |
C |
15: 91,699,686 (GRCm39) |
I2511T |
probably benign |
Het |
| Lvrn |
C |
A |
18: 47,010,036 (GRCm39) |
P395T |
possibly damaging |
Het |
| Myrip |
C |
A |
9: 120,293,764 (GRCm39) |
S753* |
probably null |
Het |
| Or14j8 |
A |
G |
17: 38,263,681 (GRCm39) |
I78T |
probably benign |
Het |
| Or52ae9 |
T |
C |
7: 103,390,207 (GRCm39) |
K80R |
probably benign |
Het |
| Pcdhb13 |
T |
C |
18: 37,576,873 (GRCm39) |
I417T |
probably damaging |
Het |
| Per2 |
T |
C |
1: 91,357,172 (GRCm39) |
T664A |
possibly damaging |
Het |
| Plec |
A |
T |
15: 76,056,962 (GRCm39) |
L4347Q |
probably damaging |
Het |
| Poln |
A |
G |
5: 34,261,295 (GRCm39) |
S561P |
probably benign |
Het |
| Polr1a |
T |
C |
6: 71,942,690 (GRCm39) |
F1177L |
probably benign |
Het |
| Pramel24 |
C |
T |
4: 143,452,850 (GRCm39) |
R94* |
probably null |
Het |
| Ptprb |
A |
T |
10: 116,189,754 (GRCm39) |
R1804S |
probably benign |
Het |
| Rhof |
C |
T |
5: 123,257,588 (GRCm39) |
V181M |
probably damaging |
Het |
| Rufy4 |
T |
C |
1: 74,186,822 (GRCm39) |
C537R |
probably damaging |
Het |
| Slc22a12 |
T |
C |
19: 6,588,818 (GRCm39) |
E281G |
probably damaging |
Het |
| Slco6b1 |
T |
A |
1: 96,915,622 (GRCm39) |
|
noncoding transcript |
Het |
| Stac |
C |
A |
9: 111,433,126 (GRCm39) |
|
probably null |
Het |
| Tcof1 |
C |
A |
18: 60,952,673 (GRCm39) |
A898S |
unknown |
Het |
| Tep1 |
C |
T |
14: 51,081,191 (GRCm39) |
R1349Q |
possibly damaging |
Het |
| Thoc6 |
A |
T |
17: 23,888,319 (GRCm39) |
|
probably benign |
Het |
| Tmem179 |
A |
T |
12: 112,477,461 (GRCm39) |
F8I |
possibly damaging |
Het |
| Tnpo3 |
A |
G |
6: 29,560,091 (GRCm39) |
L684P |
probably damaging |
Het |
| Ubash3a |
T |
C |
17: 31,456,249 (GRCm39) |
Y506H |
probably damaging |
Het |
| Umps |
G |
A |
16: 33,777,288 (GRCm39) |
Q431* |
probably null |
Het |
| Unc13c |
A |
G |
9: 73,481,289 (GRCm39) |
|
probably null |
Het |
| Vmn1r210 |
A |
T |
13: 23,011,779 (GRCm39) |
M169K |
probably benign |
Het |
| Zfp946 |
C |
T |
17: 22,673,548 (GRCm39) |
Q101* |
probably null |
Het |
|
| Other mutations in Nectin4 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00819:Nectin4
|
APN |
1 |
171,212,254 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01558:Nectin4
|
APN |
1 |
171,212,257 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL02608:Nectin4
|
APN |
1 |
171,212,341 (GRCm39) |
missense |
probably benign |
0.05 |
|
R2047:Nectin4
|
UTSW |
1 |
171,212,720 (GRCm39) |
missense |
possibly damaging |
0.61 |
|
R2203:Nectin4
|
UTSW |
1 |
171,213,797 (GRCm39) |
missense |
possibly damaging |
0.78 |
|
R2518:Nectin4
|
UTSW |
1 |
171,207,776 (GRCm39) |
missense |
probably benign |
0.00 |
|
R4708:Nectin4
|
UTSW |
1 |
171,212,714 (GRCm39) |
missense |
probably benign |
0.02 |
|
R4856:Nectin4
|
UTSW |
1 |
171,212,383 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R4886:Nectin4
|
UTSW |
1 |
171,212,383 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R5222:Nectin4
|
UTSW |
1 |
171,212,825 (GRCm39) |
splice site |
probably null |
|
|
R5264:Nectin4
|
UTSW |
1 |
171,211,273 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5661:Nectin4
|
UTSW |
1 |
171,212,738 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6466:Nectin4
|
UTSW |
1 |
171,214,321 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6714:Nectin4
|
UTSW |
1 |
171,198,218 (GRCm39) |
start gained |
probably benign |
|
|
R7272:Nectin4
|
UTSW |
1 |
171,214,212 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7302:Nectin4
|
UTSW |
1 |
171,214,203 (GRCm39) |
nonsense |
probably null |
|
|
R7318:Nectin4
|
UTSW |
1 |
171,208,031 (GRCm39) |
missense |
probably benign |
0.16 |
|
R7669:Nectin4
|
UTSW |
1 |
171,207,827 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7732:Nectin4
|
UTSW |
1 |
171,214,246 (GRCm39) |
missense |
probably benign |
0.00 |
|
R7751:Nectin4
|
UTSW |
1 |
171,211,326 (GRCm39) |
critical splice donor site |
probably null |
|
|
R7912:Nectin4
|
UTSW |
1 |
171,207,941 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R7993:Nectin4
|
UTSW |
1 |
171,211,322 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8029:Nectin4
|
UTSW |
1 |
171,214,255 (GRCm39) |
missense |
probably benign |
0.04 |
|
R8306:Nectin4
|
UTSW |
1 |
171,211,325 (GRCm39) |
missense |
probably null |
1.00 |
|
R8314:Nectin4
|
UTSW |
1 |
171,212,295 (GRCm39) |
missense |
probably benign |
0.44 |
|
R8475:Nectin4
|
UTSW |
1 |
171,212,280 (GRCm39) |
nonsense |
probably null |
|
|
R8807:Nectin4
|
UTSW |
1 |
171,211,282 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9054:Nectin4
|
UTSW |
1 |
171,214,351 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9383:Nectin4
|
UTSW |
1 |
171,213,251 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9526:Nectin4
|
UTSW |
1 |
171,210,209 (GRCm39) |
nonsense |
probably null |
|
|
R9580:Nectin4
|
UTSW |
1 |
171,211,324 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9667:Nectin4
|
UTSW |
1 |
171,210,165 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9782:Nectin4
|
UTSW |
1 |
171,214,192 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- CATATGCTCACCTTCGAGGG -3'
(R):5'- AGGTCTTGCAAGCAGGAGTG -3'
Sequencing Primer
(F):5'- GTGTAGTTTGGCAATCATACCC -3'
(R):5'- TGCAAGAGTAGCCCCAGAGC -3'
|
| Posted On |
2015-05-14 |
Incidental Mutation