Incidental Mutation 'R0413:Nid1'
ID 36823
Institutional Source Beutler Lab
Gene Symbol Nid1
Ensembl Gene ENSMUSG00000005397
Gene Name nidogen 1
Synonyms nidogen-1, entactin, entactin 1, entactin-1
MMRRC Submission 038615-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.227) question?
Stock # R0413 (G1)
Quality Score 225
Status Validated
Chromosome 13
Chromosomal Location 13612252-13686849 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 13656681 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Asparagine at position 604 (I604N)
Ref Sequence ENSEMBL: ENSMUSP00000005532 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000005532]
AlphaFold P10493
PDB Structure NIDOGEN-1 G2/PERLECAN IG3 COMPLEX [X-RAY DIFFRACTION]
DOMAIN G2 OF MOUSE NIDOGEN-1 [X-RAY DIFFRACTION]
Crystal structure of Nidogen/Laminin Complex [X-RAY DIFFRACTION]
Predicted Effect probably benign
Transcript: ENSMUST00000005532
AA Change: I604N

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000005532
Gene: ENSMUSG00000005397
AA Change: I604N

DomainStartEndE-ValueType
signal peptide 1 28 N/A INTRINSIC
NIDO 106 270 3.8e-70 SMART
low complexity region 277 296 N/A INTRINSIC
EGF 387 424 3.46e0 SMART
G2F 425 664 7.69e-153 SMART
EGF 669 707 8.65e-1 SMART
EGF_CA 708 749 4.38e-11 SMART
EGF 759 799 8.19e-2 SMART
EGF_CA 800 838 1.42e-10 SMART
TY 873 921 1.17e-19 SMART
LY 968 1010 1.35e-2 SMART
LY 1011 1053 4.34e-15 SMART
LY 1054 1098 3.34e-16 SMART
LY 1099 1141 3.25e-5 SMART
LY 1142 1181 1.08e1 SMART
EGF 1209 1242 2.45e0 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000220813
Predicted Effect noncoding transcript
Transcript: ENSMUST00000222142
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.0%
  • 20x: 94.9%
Validation Efficiency 99% (99/100)
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 nidogen family of basement membrane glycoproteins. The protein interacts with several other components of basement membranes, and may play a role in cell interactions with the extracellular matrix. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit neurologic deficits including seizure-like symptoms and loss of muscle control in the hind legs, and show altered basement membrane morphology in selected locations including brain capillaries and the lens capsule. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 97 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb11 A G 2: 69,158,355 (GRCm39) probably benign Het
Adh1 C T 3: 137,986,193 (GRCm39) T60I probably benign Het
Agtpbp1 T A 13: 59,661,966 (GRCm39) I282F probably damaging Het
Arih2 G T 9: 108,493,916 (GRCm39) Q166K probably damaging Het
Cacna1s A G 1: 136,025,947 (GRCm39) T1031A probably benign Het
Ccdc102a C A 8: 95,629,914 (GRCm39) E542D probably benign Het
Cdk1 T C 10: 69,180,929 (GRCm39) I94V probably benign Het
Cep290 C T 10: 100,359,176 (GRCm39) Q969* probably null Het
Cilp2 A G 8: 70,335,643 (GRCm39) S452P probably benign Het
Col12a1 T C 9: 79,606,642 (GRCm39) T594A probably damaging Het
Cpox A G 16: 58,491,232 (GRCm39) T148A possibly damaging Het
Csf3r A G 4: 125,933,460 (GRCm39) probably benign Het
Csmd1 A T 8: 16,760,530 (GRCm39) C202S probably damaging Het
Dlgap4 T C 2: 156,604,746 (GRCm39) S261P probably damaging Het
Dnah9 T A 11: 65,998,961 (GRCm39) Y1029F probably damaging Het
Dok5 T C 2: 170,671,880 (GRCm39) probably benign Het
Dusp11 A T 6: 85,929,352 (GRCm39) probably benign Het
Edar T C 10: 58,465,262 (GRCm39) N34D probably benign Het
Efcab7 C T 4: 99,766,943 (GRCm39) T56I probably damaging Het
Entpd1 G A 19: 40,699,729 (GRCm39) V47I probably benign Het
Ephx4 A G 5: 107,551,601 (GRCm39) N62S probably benign Het
Etaa1 A T 11: 17,896,350 (GRCm39) L589* probably null Het
Fam135b T A 15: 71,335,670 (GRCm39) N508I probably benign Het
Fam193a T C 5: 34,623,552 (GRCm39) V27A possibly damaging Het
Fmnl1 A G 11: 103,084,889 (GRCm39) probably benign Het
Fstl1 A C 16: 37,641,516 (GRCm39) probably null Het
Gbp4 G A 5: 105,268,972 (GRCm39) R394C possibly damaging Het
Gemin4 T C 11: 76,102,148 (GRCm39) Y871C probably benign Het
Get1 T G 16: 95,954,217 (GRCm39) S105R probably benign Het
Gm7247 T C 14: 51,760,929 (GRCm39) V166A probably benign Het
Gpcpd1 A T 2: 132,406,543 (GRCm39) probably benign Het
Gpnmb A G 6: 49,019,737 (GRCm39) D36G probably benign Het
Ido2 C T 8: 25,048,159 (GRCm39) probably null Het
Igfn1 G A 1: 135,895,334 (GRCm39) T1744I probably benign Het
Inf2 T G 12: 112,568,110 (GRCm39) F221V probably damaging Het
Itga10 T A 3: 96,556,375 (GRCm39) I170N probably damaging Het
Lrp6 A T 6: 134,484,587 (GRCm39) D345E probably damaging Het
Macf1 A T 4: 123,366,062 (GRCm39) S2900T probably benign Het
Med13 C A 11: 86,190,033 (GRCm39) probably benign Het
Morc3 T C 16: 93,667,362 (GRCm39) V507A probably damaging Het
Myadm AC ACC 7: 3,345,276 (GRCm39) probably null Het
Myl6 C T 10: 128,328,091 (GRCm39) probably benign Het
Mylk T C 16: 34,742,314 (GRCm39) V942A probably benign Het
Myorg G T 4: 41,498,585 (GRCm39) H348Q probably benign Het
Ncdn G T 4: 126,644,327 (GRCm39) T165K possibly damaging Het
Ncf1 T C 5: 134,251,656 (GRCm39) probably benign Het
Neb T C 2: 52,180,751 (GRCm39) probably benign Het
Nsrp1 T C 11: 76,936,997 (GRCm39) R400G probably benign Het
Nup43 T G 10: 7,546,791 (GRCm39) I137S probably benign Het
Nynrin A G 14: 56,109,648 (GRCm39) N1585S possibly damaging Het
Obscn T A 11: 58,893,823 (GRCm39) Y6748F probably benign Het
Omg A G 11: 79,393,661 (GRCm39) S66P possibly damaging Het
Or13a27 A T 7: 139,925,108 (GRCm39) S265T possibly damaging Het
Or2y1d T C 11: 49,322,212 (GRCm39) V303A possibly damaging Het
Or4c15 A G 2: 88,759,906 (GRCm39) V251A probably benign Het
Or51b6b A T 7: 103,309,957 (GRCm39) F167I possibly damaging Het
Or52z1 A G 7: 103,437,362 (GRCm39) Y41H probably damaging Het
Or5ak22 T C 2: 85,230,019 (GRCm39) N286S probably damaging Het
Or8g27 A G 9: 39,129,566 (GRCm39) I304M probably benign Het
Or8k24 G A 2: 86,216,058 (GRCm39) R235C probably benign Het
Ormdl1 C T 1: 53,347,978 (GRCm39) probably benign Het
Ovch2 T A 7: 107,381,243 (GRCm39) I552L probably benign Het
Pcare T G 17: 72,059,212 (GRCm39) D155A probably benign Het
Pcsk9 G T 4: 106,311,538 (GRCm39) T231N probably damaging Het
Pgpep1 T C 8: 71,110,100 (GRCm39) N22S probably damaging Het
Plb1 T C 5: 32,512,706 (GRCm39) F1355L probably damaging Het
Plcg1 G T 2: 160,603,349 (GRCm39) L1173F probably damaging Het
Plch2 A T 4: 155,091,373 (GRCm39) probably null Het
Ppp1r3g T A 13: 36,153,331 (GRCm39) F250L probably damaging Het
Prkcg A G 7: 3,368,095 (GRCm39) I381V probably benign Het
Pum2 C T 12: 8,763,464 (GRCm39) A207V probably benign Het
Rabac1 T C 7: 24,669,607 (GRCm39) E166G probably damaging Het
Rad21l G A 2: 151,493,851 (GRCm39) S450L probably benign Het
Rangap1 ACACTCA ACA 15: 81,600,876 (GRCm39) probably null Het
Reg3b G T 6: 78,348,824 (GRCm39) C40F probably damaging Het
Rfx2 A G 17: 57,091,418 (GRCm39) probably benign Het
Rrp15 G A 1: 186,481,346 (GRCm39) probably benign Het
Schip1 G T 3: 68,401,946 (GRCm39) G36C probably damaging Het
Sec61a2 A T 2: 5,881,165 (GRCm39) probably benign Het
Sema5a A G 15: 32,669,590 (GRCm39) K705E probably damaging Het
Setx A G 2: 29,029,290 (GRCm39) Y186C probably damaging Het
Slc22a23 T C 13: 34,367,115 (GRCm39) E631G probably damaging Het
Slc5a5 T C 8: 71,344,319 (GRCm39) T134A possibly damaging Het
Stx7 T C 10: 24,057,492 (GRCm39) S173P probably damaging Het
Sybu T C 15: 44,536,668 (GRCm39) T353A probably damaging Het
Syde2 T A 3: 145,712,887 (GRCm39) N1008K probably damaging Het
Tiam1 T C 16: 89,606,253 (GRCm39) probably benign Het
Timm10b G A 7: 105,327,537 (GRCm39) E61K probably benign Het
Tm2d1 A G 4: 98,253,810 (GRCm39) I121T probably damaging Het
Trim75 T C 8: 65,435,892 (GRCm39) E186G probably benign Het
Tti1 T C 2: 157,837,396 (GRCm39) K895E probably benign Het
Vmn1r43 A G 6: 89,846,830 (GRCm39) S219P probably damaging Het
Vmn2r73 A T 7: 85,521,087 (GRCm39) S294T possibly damaging Het
Vmn2r94 A T 17: 18,464,080 (GRCm39) F737I probably damaging Het
Vsx2 A T 12: 84,616,777 (GRCm39) T21S probably benign Het
Zfp462 G T 4: 55,010,534 (GRCm39) R833S probably damaging Het
Zfpl1 G A 19: 6,132,482 (GRCm39) P143L probably damaging Het
Other mutations in Nid1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00092:Nid1 APN 13 13,650,977 (GRCm39) missense probably damaging 1.00
IGL02126:Nid1 APN 13 13,663,743 (GRCm39) splice site probably null
IGL02452:Nid1 APN 13 13,683,305 (GRCm39) missense probably benign 0.17
IGL02806:Nid1 APN 13 13,642,897 (GRCm39) missense probably benign 0.00
IGL02966:Nid1 APN 13 13,656,806 (GRCm39) missense probably benign 0.09
IGL03136:Nid1 APN 13 13,675,084 (GRCm39) missense probably benign 0.33
IGL03411:Nid1 APN 13 13,612,474 (GRCm39) missense probably damaging 0.98
R0384:Nid1 UTSW 13 13,638,421 (GRCm39) missense probably benign 0.34
R1257:Nid1 UTSW 13 13,658,375 (GRCm39) missense probably benign 0.01
R1390:Nid1 UTSW 13 13,650,831 (GRCm39) missense probably damaging 1.00
R1397:Nid1 UTSW 13 13,683,380 (GRCm39) missense possibly damaging 0.94
R2057:Nid1 UTSW 13 13,675,058 (GRCm39) missense probably benign 0.00
R2058:Nid1 UTSW 13 13,675,058 (GRCm39) missense probably benign 0.00
R2059:Nid1 UTSW 13 13,675,058 (GRCm39) missense probably benign 0.00
R2132:Nid1 UTSW 13 13,684,071 (GRCm39) missense probably benign 0.04
R2140:Nid1 UTSW 13 13,674,253 (GRCm39) missense probably damaging 1.00
R2195:Nid1 UTSW 13 13,650,788 (GRCm39) missense probably damaging 1.00
R2237:Nid1 UTSW 13 13,675,070 (GRCm39) missense probably benign
R2312:Nid1 UTSW 13 13,675,078 (GRCm39) missense probably benign 0.15
R2987:Nid1 UTSW 13 13,674,258 (GRCm39) missense probably benign 0.40
R3696:Nid1 UTSW 13 13,661,344 (GRCm39) missense probably damaging 0.99
R3697:Nid1 UTSW 13 13,661,344 (GRCm39) missense probably damaging 0.99
R3698:Nid1 UTSW 13 13,661,344 (GRCm39) missense probably damaging 0.99
R3772:Nid1 UTSW 13 13,651,003 (GRCm39) splice site probably benign
R4092:Nid1 UTSW 13 13,661,224 (GRCm39) missense probably damaging 0.96
R4126:Nid1 UTSW 13 13,650,957 (GRCm39) missense probably damaging 1.00
R4128:Nid1 UTSW 13 13,650,957 (GRCm39) missense probably damaging 1.00
R4680:Nid1 UTSW 13 13,647,437 (GRCm39) missense probably damaging 1.00
R4717:Nid1 UTSW 13 13,681,086 (GRCm39) missense probably benign 0.00
R4783:Nid1 UTSW 13 13,674,326 (GRCm39) missense probably damaging 0.97
R4812:Nid1 UTSW 13 13,681,053 (GRCm39) nonsense probably null
R4834:Nid1 UTSW 13 13,683,408 (GRCm39) missense probably damaging 1.00
R4915:Nid1 UTSW 13 13,674,171 (GRCm39) missense possibly damaging 0.89
R4930:Nid1 UTSW 13 13,684,596 (GRCm39) missense probably damaging 1.00
R5101:Nid1 UTSW 13 13,658,339 (GRCm39) missense probably damaging 1.00
R5276:Nid1 UTSW 13 13,643,157 (GRCm39) missense probably damaging 0.99
R5427:Nid1 UTSW 13 13,658,268 (GRCm39) missense probably damaging 1.00
R5447:Nid1 UTSW 13 13,612,495 (GRCm39) missense probably benign 0.00
R5507:Nid1 UTSW 13 13,663,622 (GRCm39) nonsense probably null
R5663:Nid1 UTSW 13 13,647,419 (GRCm39) missense probably damaging 1.00
R5868:Nid1 UTSW 13 13,663,742 (GRCm39) critical splice donor site probably null
R6313:Nid1 UTSW 13 13,638,367 (GRCm39) missense probably benign 0.01
R6761:Nid1 UTSW 13 13,656,620 (GRCm39) missense probably benign 0.22
R7069:Nid1 UTSW 13 13,683,353 (GRCm39) missense probably benign
R7208:Nid1 UTSW 13 13,642,970 (GRCm39) missense probably benign 0.01
R7284:Nid1 UTSW 13 13,663,675 (GRCm39) missense probably benign 0.01
R7434:Nid1 UTSW 13 13,643,049 (GRCm39) missense probably benign
R7449:Nid1 UTSW 13 13,656,636 (GRCm39) missense probably damaging 1.00
R7574:Nid1 UTSW 13 13,643,028 (GRCm39) missense probably benign
R7762:Nid1 UTSW 13 13,663,630 (GRCm39) missense probably damaging 1.00
R7887:Nid1 UTSW 13 13,674,318 (GRCm39) missense possibly damaging 0.83
R8420:Nid1 UTSW 13 13,612,416 (GRCm39) missense possibly damaging 0.81
R8506:Nid1 UTSW 13 13,650,759 (GRCm39) missense probably damaging 0.99
R8756:Nid1 UTSW 13 13,683,386 (GRCm39) missense probably benign 0.32
R8903:Nid1 UTSW 13 13,638,515 (GRCm39) missense probably benign 0.00
R9084:Nid1 UTSW 13 13,652,925 (GRCm39) critical splice donor site probably null
R9297:Nid1 UTSW 13 13,650,897 (GRCm39) missense possibly damaging 0.92
R9344:Nid1 UTSW 13 13,652,894 (GRCm39) missense probably damaging 1.00
R9552:Nid1 UTSW 13 13,677,045 (GRCm39) missense probably damaging 0.99
X0028:Nid1 UTSW 13 13,684,119 (GRCm39) missense probably benign 0.14
Predicted Primers PCR Primer
(F):5'- GGCAGGAACCGCTCACTACTAATG -3'
(R):5'- TTGCCAAGAGCCACTGATGACC -3'

Sequencing Primer
(F):5'- GCTCACTACTAATGTCCTCAAGG -3'
(R):5'- ATGTCCAGCCTGCATGAG -3'
Posted On 2013-05-09