Incidental Mutation 'R9054:Nectin4'
| ID |
688544 |
| 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 |
068880-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.079)
|
| Stock # |
R9054 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
1 |
| Chromosomal Location |
171197741-171215855 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 171214351 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Isoleucine
at position 502
(N502I)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000006578
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006578]
[ENSMUST00000056449]
[ENSMUST00000094325]
[ENSMUST00000111286]
|
| AlphaFold |
Q8R007 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000006578
AA Change: N502I
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000006578
Gene: ENSMUSG00000006411
AA Change: N502I
| 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 damaging
Transcript: ENSMUST00000094325
AA Change: N477I
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000091883
Gene: ENSMUSG00000006411
AA Change: N477I
| 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 damaging
Transcript: ENSMUST00000111286
AA Change: N502I
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000106917
Gene: ENSMUSG00000006411
AA Change: N502I
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 99.1%
|
| Validation Efficiency |
98% (51/52) |
| 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: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Ankef1 |
T |
A |
2: 136,395,594 (GRCm39) |
D641E |
probably benign |
Het |
| Anln |
A |
G |
9: 22,272,116 (GRCm39) |
|
probably null |
Het |
| Areg |
A |
T |
5: 91,292,217 (GRCm39) |
E172D |
probably damaging |
Het |
| Ccdc51 |
A |
T |
9: 108,918,482 (GRCm39) |
T24S |
probably benign |
Het |
| Cckar |
A |
T |
5: 53,860,424 (GRCm39) |
I135N |
probably damaging |
Het |
| Cdca7 |
CGAGGAAGAGGAGGAGGAAGAGGAGGAGGAAGAGGA |
CGAGGAAGAGGAGGAGGAAGAGGA |
2: 72,313,821 (GRCm39) |
|
probably benign |
Het |
| Cep295 |
T |
C |
9: 15,235,551 (GRCm39) |
H2056R |
possibly damaging |
Het |
| Chrnb2 |
T |
C |
3: 89,664,562 (GRCm39) |
K451E |
probably damaging |
Het |
| Ctnna2 |
C |
T |
6: 76,919,249 (GRCm39) |
R663Q |
probably benign |
Het |
| Cyp4f37 |
A |
T |
17: 32,853,253 (GRCm39) |
I406F |
probably benign |
Het |
| Eml4 |
T |
A |
17: 83,734,640 (GRCm39) |
|
probably benign |
Het |
| Fkrp |
G |
T |
7: 16,544,569 (GRCm39) |
T431K |
probably damaging |
Het |
| Fsip2 |
A |
T |
2: 82,806,180 (GRCm39) |
Y833F |
possibly damaging |
Het |
| Galnt2 |
T |
C |
8: 125,058,837 (GRCm39) |
|
probably null |
Het |
| Gm8180 |
T |
A |
14: 44,019,806 (GRCm39) |
|
probably null |
Het |
| Hcn1 |
T |
C |
13: 118,108,171 (GRCm39) |
S552P |
unknown |
Het |
| Ifit1 |
A |
C |
19: 34,625,887 (GRCm39) |
E341A |
possibly damaging |
Het |
| Iyd |
A |
G |
10: 3,490,250 (GRCm39) |
|
probably benign |
Het |
| Krt72 |
A |
T |
15: 101,694,836 (GRCm39) |
S20T |
probably damaging |
Het |
| Lemd2 |
G |
T |
17: 27,423,069 (GRCm39) |
D108E |
probably benign |
Het |
| Lipn |
A |
T |
19: 34,054,376 (GRCm39) |
I205F |
possibly damaging |
Het |
| Nat1 |
G |
T |
8: 67,943,723 (GRCm39) |
R36L |
probably benign |
Het |
| Nebl |
A |
T |
2: 17,415,907 (GRCm39) |
M334K |
possibly damaging |
Het |
| Nrp1 |
G |
A |
8: 129,214,389 (GRCm39) |
V626I |
probably benign |
Het |
| Oprm1 |
G |
A |
10: 6,773,914 (GRCm39) |
|
probably benign |
Het |
| Or52w1 |
A |
G |
7: 105,017,680 (GRCm39) |
Y49C |
probably damaging |
Het |
| Or8a1b |
C |
T |
9: 37,623,204 (GRCm39) |
V124M |
probably damaging |
Het |
| Pde2a |
A |
G |
7: 101,156,927 (GRCm39) |
Y637C |
probably damaging |
Het |
| Pde4d |
T |
C |
13: 110,071,924 (GRCm39) |
V306A |
probably damaging |
Het |
| Pdzd9 |
G |
A |
7: 120,269,498 (GRCm39) |
|
probably benign |
Het |
| Pitpnm3 |
T |
A |
11: 71,947,017 (GRCm39) |
D810V |
probably damaging |
Het |
| Pkd1l3 |
A |
T |
8: 110,392,304 (GRCm39) |
H1966L |
probably benign |
Het |
| Pmfbp1 |
C |
T |
8: 110,247,661 (GRCm39) |
T319I |
possibly damaging |
Het |
| Pramel28 |
T |
C |
4: 143,692,314 (GRCm39) |
Q229R |
probably benign |
Het |
| Prb1c |
G |
C |
6: 132,338,856 (GRCm39) |
Q121E |
unknown |
Het |
| Psg18 |
T |
A |
7: 18,087,450 (GRCm39) |
R69S |
possibly damaging |
Het |
| Ptprg |
A |
T |
14: 12,213,638 (GRCm38) |
Q1002L |
possibly damaging |
Het |
| Ptprj |
T |
C |
2: 90,290,984 (GRCm39) |
Y585C |
probably damaging |
Het |
| Rad51c |
T |
C |
11: 87,293,542 (GRCm39) |
T105A |
probably benign |
Het |
| Rbm12 |
A |
T |
2: 155,937,481 (GRCm39) |
D930E |
unknown |
Het |
| Rlf |
A |
C |
4: 121,007,784 (GRCm39) |
S509A |
possibly damaging |
Het |
| Slc39a3 |
C |
A |
10: 80,869,499 (GRCm39) |
G53C |
probably damaging |
Het |
| Smchd1 |
G |
A |
17: 71,670,017 (GRCm39) |
Q1685* |
probably null |
Het |
| Sprr2d |
A |
C |
3: 92,247,715 (GRCm39) |
E52A |
unknown |
Het |
| Stat1 |
A |
G |
1: 52,182,086 (GRCm39) |
N355S |
probably damaging |
Het |
| Tmem30b |
T |
C |
12: 73,592,923 (GRCm39) |
E64G |
probably benign |
Het |
| Ttll11 |
A |
T |
2: 35,869,392 (GRCm39) |
V82D |
probably benign |
Het |
| Ttn |
T |
A |
2: 76,570,977 (GRCm39) |
T26639S |
probably damaging |
Het |
| Usp53 |
A |
T |
3: 122,727,725 (GRCm39) |
N952K |
probably benign |
Het |
| Vmn1r199 |
T |
A |
13: 22,567,724 (GRCm39) |
H339Q |
possibly damaging |
Het |
| Vps13b |
G |
A |
15: 35,422,537 (GRCm39) |
D166N |
probably damaging |
Het |
| Zfp954 |
C |
A |
7: 7,119,097 (GRCm39) |
C149F |
probably benign |
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 |
|
R4125:Nectin4
|
UTSW |
1 |
171,213,301 (GRCm39) |
missense |
probably benign |
0.02 |
|
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 |
|
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'- CCACGTTAACCACAGTGAGAGAG -3'
(R):5'- AGGATGACCTACACACAATGG -3'
Sequencing Primer
(F):5'- GATCGAGACACAGACCGAACTG -3'
(R):5'- GGAGCTCTCCTGATGAACAG -3'
|
| Posted On |
2021-11-19 |
Incidental Mutation