Incidental Mutation 'R9459:Nectin1'
ID 714766
Institutional Source Beutler Lab
Gene Symbol Nectin1
Ensembl Gene ENSMUSG00000032012
Gene Name nectin cell adhesion molecule 1
Synonyms nectin-1, PRR1, HIgR, HveC, Cd111, PRR, Pvrl1
MMRRC Submission
Accession Numbers
Essential gene? Probably essential (E-score: 0.809) question?
Stock # R9459 (G1)
Quality Score 225.009
Status Not validated
Chromosome 9
Chromosomal Location 43655251-43718758 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 43715090 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Alanine at position 442 (E442A)
Ref Sequence ENSEMBL: ENSMUSP00000034510 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034510] [ENSMUST00000216893]
AlphaFold Q9JKF6
PDB Structure Solution structure of the third Immunoglobulin-like domain of nectin-1 [SOLUTION NMR]
Predicted Effect probably benign
Transcript: ENSMUST00000034510
AA Change: E442A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000034510
Gene: ENSMUSG00000032012
AA Change: E442A

low complexity region 1 20 N/A INTRINSIC
IG 36 143 8.51e-7 SMART
Pfam:C2-set_2 148 237 8.5e-21 PFAM
IG 254 334 1.28e-1 SMART
transmembrane domain 355 377 N/A INTRINSIC
low complexity region 436 448 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000216893
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 98.9%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an adhesion protein that plays a role in the organization of adherens junctions and tight junctions in epithelial and endothelial cells. The protein is a calcium(2+)-independent cell-cell adhesion molecule that belongs to the immunoglobulin superfamily and has 3 extracellular immunoglobulin-like loops, a single transmembrane domain (in some isoforms), and a cytoplasmic region. This protein acts as a receptor for glycoprotein D (gD) of herpes simplex viruses 1 and 2 (HSV-1, HSV-2), and pseudorabies virus (PRV) and mediates viral entry into epithelial and neuronal cells. Mutations in this gene cause cleft lip and palate/ectodermal dysplasia 1 syndrome (CLPED1) as well as non-syndromic cleft lip with or without cleft palate (CL/P). Alternative splicing results in multiple transcript variants encoding proteins with distinct C-termini. [provided by RefSeq, Oct 2009]
PHENOTYPE: Homozygous null mice exhibit eye abnormalities including microphthalmia, absent vitreous body, abnormal ciliary body, retinal layers, and lenses, and open eyelids at birth. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb1a T A 5: 8,735,414 (GRCm39) probably null Het
Alms1 T A 6: 85,604,946 (GRCm39) C2199S probably damaging Het
Aox3 A G 1: 58,189,468 (GRCm39) I390V probably benign Het
Ap3b2 T C 7: 81,123,651 (GRCm39) N400S probably benign Het
Baalc A T 15: 38,797,419 (GRCm39) N70I probably benign Het
Brca2 T A 5: 150,464,094 (GRCm39) V1286D probably damaging Het
Ccdc30 T C 4: 119,234,470 (GRCm39) R81G possibly damaging Het
Cd209g T C 8: 4,185,610 (GRCm39) S15P probably benign Het
Chrnb3 G A 8: 27,883,884 (GRCm39) W207* probably null Het
Cmpk2 C T 12: 26,528,022 (GRCm39) T413M probably damaging Het
Coq4 T A 2: 29,678,562 (GRCm39) Y63N probably damaging Het
Depdc5 T A 5: 33,148,117 (GRCm39) S1478T probably damaging Het
Etf1 A G 18: 35,039,134 (GRCm39) F378L probably benign Het
Exoc6 T C 19: 37,574,341 (GRCm39) V324A probably benign Het
Frem2 A G 3: 53,560,907 (GRCm39) L1200P probably benign Het
Gadl1 T C 9: 115,794,679 (GRCm39) W285R probably damaging Het
Gbp3 A G 3: 142,270,707 (GRCm39) probably null Het
Gm14295 C T 2: 176,499,165 (GRCm39) T5I possibly damaging Het
Hps4 T C 5: 112,522,875 (GRCm39) S578P probably benign Het
Kctd13 T A 7: 126,544,254 (GRCm39) D317E probably damaging Het
Kdm4b T A 17: 56,706,509 (GRCm39) D881E probably benign Het
Klf10 G A 15: 38,296,171 (GRCm39) P473L probably damaging Het
Lrch3 A T 16: 32,799,775 (GRCm39) D371V probably damaging Het
Msh2 T C 17: 87,985,758 (GRCm39) S112P possibly damaging Het
Msh3 A G 13: 92,352,047 (GRCm39) V1036A possibly damaging Het
Mybl1 A G 1: 9,746,484 (GRCm39) V392A possibly damaging Het
Myo7a T C 7: 97,722,380 (GRCm39) I1182V possibly damaging Het
Nscme3l T A 19: 5,553,757 (GRCm39) H8L probably benign Het
Obsl1 G T 1: 75,474,884 (GRCm39) H839N probably benign Het
Or4c105 T C 2: 88,647,967 (GRCm39) F151L probably benign Het
Or9i1b T C 19: 13,896,674 (GRCm39) C97R possibly damaging Het
Pacs1 C T 19: 5,195,098 (GRCm39) probably null Het
Pcdh17 G T 14: 84,686,063 (GRCm39) E843D probably benign Het
Pcnt A G 10: 76,228,572 (GRCm39) L1531P probably damaging Het
Pdgfra A G 5: 75,353,129 (GRCm39) D973G probably damaging Het
Pkd2 A G 5: 104,614,800 (GRCm39) Y214C probably damaging Het
Plcb1 T C 2: 135,164,558 (GRCm39) Y427H probably benign Het
Ppm1h A G 10: 122,743,482 (GRCm39) N402S possibly damaging Het
Rassf4 T A 6: 116,618,749 (GRCm39) probably null Het
Ryr1 G A 7: 28,768,068 (GRCm39) T2856I probably damaging Het
Serpinb8 A T 1: 107,533,520 (GRCm39) K192* probably null Het
Slfn14 T G 11: 83,170,198 (GRCm39) Q482P possibly damaging Het
Spata2 A G 2: 167,327,205 (GRCm39) V64A probably benign Het
Tax1bp1 T G 6: 52,706,314 (GRCm39) V105G probably damaging Het
Tbc1d22a T G 15: 86,120,021 (GRCm39) S142A possibly damaging Het
Tdrd9 T C 12: 111,992,007 (GRCm39) F594S probably damaging Het
Uba3 T C 6: 97,166,559 (GRCm39) I281V probably benign Het
Uggt2 T C 14: 119,286,595 (GRCm39) E723G probably benign Het
Usp20 C T 2: 30,901,024 (GRCm39) S391F probably damaging Het
Usp24 T A 4: 106,199,555 (GRCm39) D166E probably damaging Het
Vmn1r1 A G 1: 181,985,503 (GRCm39) V54A probably benign Het
Zfp442 T A 2: 150,250,668 (GRCm39) E411D unknown Het
Zfp804a T C 2: 82,089,753 (GRCm39) I1194T probably damaging Het
Other mutations in Nectin1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01618:Nectin1 APN 9 43,702,555 (GRCm39) nonsense probably null
IGL01939:Nectin1 APN 9 43,703,871 (GRCm39) unclassified probably benign
IGL01978:Nectin1 APN 9 43,703,444 (GRCm39) missense probably damaging 0.99
IGL02795:Nectin1 APN 9 43,714,849 (GRCm39) missense probably benign
K3955:Nectin1 UTSW 9 43,703,375 (GRCm39) missense probably damaging 1.00
R0563:Nectin1 UTSW 9 43,702,342 (GRCm39) missense probably benign
R1439:Nectin1 UTSW 9 43,703,396 (GRCm39) missense possibly damaging 0.78
R1822:Nectin1 UTSW 9 43,702,374 (GRCm39) nonsense probably null
R4356:Nectin1 UTSW 9 43,703,802 (GRCm39) missense probably benign 0.22
R5153:Nectin1 UTSW 9 43,714,795 (GRCm39) missense probably damaging 0.99
R5516:Nectin1 UTSW 9 43,715,090 (GRCm39) missense probably benign 0.03
R5864:Nectin1 UTSW 9 43,702,607 (GRCm39) missense probably damaging 1.00
R6903:Nectin1 UTSW 9 43,703,179 (GRCm39) missense possibly damaging 0.95
R7791:Nectin1 UTSW 9 43,703,336 (GRCm39) missense probably benign 0.08
R7878:Nectin1 UTSW 9 43,715,198 (GRCm39) missense probably benign 0.10
R8046:Nectin1 UTSW 9 43,703,798 (GRCm39) missense probably benign 0.00
R8945:Nectin1 UTSW 9 43,703,237 (GRCm39) missense probably benign
R9526:Nectin1 UTSW 9 43,702,369 (GRCm39) missense probably benign
R9744:Nectin1 UTSW 9 43,715,240 (GRCm39) missense probably damaging 0.97
Predicted Primers PCR Primer

Sequencing Primer
Posted On 2022-06-15