Incidental Mutation 'R4708:Nectin4'
ID 355390
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 042017-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.079) question?
Stock # R4708 (G1)
Quality Score 225
Status Validated
Chromosome 1
Chromosomal Location 171197741-171215855 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 171212714 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 349 (I349T)
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: I349T

PolyPhen 2 Score 0.020 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000006578
Gene: ENSMUSG00000006411
AA Change: I349T

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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: I349T

PolyPhen 2 Score 0.020 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000091883
Gene: ENSMUSG00000006411
AA Change: I349T

DomainStartEndE-ValueType
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: I349T

PolyPhen 2 Score 0.020 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000106917
Gene: ENSMUSG00000006411
AA Change: I349T

DomainStartEndE-ValueType
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 0.0898 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.8%
Validation Efficiency 97% (68/70)
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: 67 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2610021A01Rik G A 7: 41,261,309 (GRCm39) G2D probably damaging Het
4930505A04Rik T C 11: 30,404,717 (GRCm39) Y62C probably damaging Het
Aadacl4 A C 4: 144,349,899 (GRCm39) K385N probably benign Het
Abcb4 A T 5: 8,965,125 (GRCm39) T332S possibly damaging Het
Aco2 G A 15: 81,794,117 (GRCm39) probably null Het
Aplf G T 6: 87,640,739 (GRCm39) S69Y probably damaging Het
Arhgap27 A G 11: 103,224,388 (GRCm39) probably benign Het
B4galnt1 T A 10: 127,005,684 (GRCm39) Y262N probably damaging Het
Bag4 C T 8: 26,259,516 (GRCm39) A228T probably benign Het
Ccdc62 T G 5: 124,068,925 (GRCm39) probably null Het
Cd109 T A 9: 78,579,871 (GRCm39) I649K probably benign Het
Cd209b T C 8: 3,974,215 (GRCm39) E99G probably damaging Het
Cep290 A G 10: 100,359,126 (GRCm39) K952R probably benign Het
Ces2a A G 8: 105,463,938 (GRCm39) H190R probably benign Het
Clec14a A G 12: 58,314,489 (GRCm39) S378P probably benign Het
Col27a1 A G 4: 63,202,150 (GRCm39) Q947R probably benign Het
Dennd3 A G 15: 73,395,344 (GRCm39) T146A probably damaging Het
Dpy19l4 T A 4: 11,277,970 (GRCm39) M486L probably benign Het
Dysf C A 6: 84,074,697 (GRCm39) D499E probably damaging Het
Eif4enif1 T G 11: 3,170,323 (GRCm39) H125Q probably damaging Het
Fcgbp A T 7: 27,794,386 (GRCm39) M1197L probably benign Het
Fubp3 C T 2: 31,498,122 (GRCm39) T92I probably benign Het
Gm19426 T C 2: 84,573,803 (GRCm39) probably null Het
Gtf2ird2 A G 5: 134,245,140 (GRCm39) H466R probably damaging Het
Hdac5 T C 11: 102,093,019 (GRCm39) S573G probably damaging Het
Iars2 A T 1: 185,021,554 (GRCm39) M916K probably benign Het
Insr A T 8: 3,261,346 (GRCm39) probably benign Het
Itgam T C 7: 127,700,709 (GRCm39) V493A probably damaging Het
Ivl T A 3: 92,479,057 (GRCm39) K336I probably damaging Het
Kcng2 A G 18: 80,366,067 (GRCm39) I95T probably damaging Het
Lap3 A G 5: 45,668,480 (GRCm39) R431G probably damaging Het
Lrrc66 T C 5: 73,787,005 (GRCm39) H115R probably benign Het
Morc3 T C 16: 93,670,126 (GRCm39) V767A probably benign Het
Mttp A G 3: 137,839,859 (GRCm39) probably benign Het
Myo1c C T 11: 75,560,856 (GRCm39) R770* probably null Het
Nat9 G A 11: 115,074,269 (GRCm39) T133M probably damaging Het
Nlrp4a A G 7: 26,163,533 (GRCm39) E900G probably benign Het
Nlrp9c A T 7: 26,084,265 (GRCm39) M438K probably benign Het
Or2y14 T A 11: 49,405,216 (GRCm39) Y250* probably null Het
Or52p2 A T 7: 102,237,043 (GRCm39) D302E probably benign Het
Or5b21 A T 19: 12,839,261 (GRCm39) I41F probably benign Het
Parp6 T C 9: 59,549,052 (GRCm39) I507T probably damaging Het
Pde6c G A 19: 38,169,341 (GRCm39) E804K possibly damaging Het
Plscr2 A G 9: 92,173,067 (GRCm39) Y203C probably damaging Het
Ptprs A G 17: 56,735,067 (GRCm39) W216R probably damaging Het
Rhof T A 5: 123,258,454 (GRCm39) T126S probably benign Het
Riox2 A G 16: 59,296,045 (GRCm39) I49V probably benign Het
Rlig1 T C 10: 100,414,243 (GRCm39) I139V probably benign Het
Rusf1 A G 7: 127,873,852 (GRCm39) V345A probably benign Het
Shld2 A G 14: 33,989,790 (GRCm39) V372A probably benign Het
Spata31e2 A T 1: 26,723,521 (GRCm39) V553D possibly damaging Het
Tmc6 A T 11: 117,659,774 (GRCm39) C750S probably benign Het
Tmem231 C A 8: 112,660,418 (GRCm39) probably benign Het
Tmem94 T A 11: 115,677,121 (GRCm39) I131N possibly damaging Het
Tmx3 T C 18: 90,539,163 (GRCm39) probably null Het
Tnfrsf21 C T 17: 43,349,123 (GRCm39) T245I possibly damaging Het
Ttbk2 C A 2: 120,570,342 (GRCm39) R1201S probably damaging Het
Vmn2r102 A T 17: 19,914,576 (GRCm39) M714L probably benign Het
Vmn2r109 A G 17: 20,761,605 (GRCm39) L584S probably damaging Het
Vmn2r53 T A 7: 12,335,129 (GRCm39) H177L probably benign Het
Vnn1 T A 10: 23,773,250 (GRCm39) D92E probably benign Het
Zan T C 5: 137,444,974 (GRCm39) I1762V unknown Het
Zbtb20 G T 16: 43,431,039 (GRCm39) A517S probably damaging Het
Zfhx4 A G 3: 5,310,563 (GRCm39) probably null Het
Zfp560 T C 9: 20,263,214 (GRCm39) E54G possibly damaging Het
Zfp719 C T 7: 43,239,656 (GRCm39) H415Y probably damaging Het
Zmynd11 A C 13: 9,745,789 (GRCm39) V188G probably damaging Het
Other mutations in Nectin4
AlleleSourceChrCoordTypePredicted EffectPPH 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
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'- GGATTAAGCTGAGTGGGTAGC -3'
(R):5'- CTCTGCCCACCTCACGAGA -3'

Sequencing Primer
(F):5'- AGCTGTGGATGTGTCTGTCCC -3'
(R):5'- GAGACCACACGGCCTCCTTTC -3'
Posted On 2015-10-21