Incidental Mutation 'R5868:Nid1'
ID 454293
Institutional Source Beutler Lab
Gene Symbol Nid1
Ensembl Gene ENSMUSG00000005397
Gene Name nidogen 1
Synonyms nidogen-1, entactin, entactin 1, entactin-1
MMRRC Submission 044076-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.227) question?
Stock # R5868 (G1)
Quality Score 225
Status Validated
Chromosome 13
Chromosomal Location 13612252-13686849 bp(+) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) T to C at 13663742 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
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 null
Transcript: ENSMUST00000005532
SMART Domains Protein: ENSMUSP00000005532
Gene: ENSMUSG00000005397

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: ENSMUST00000222142
Meta Mutation Damage Score 0.9485 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.2%
  • 20x: 90.8%
Validation Efficiency 95% (58/61)
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: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2810408A11Rik C A 11: 69,788,401 (GRCm39) K394N possibly damaging Het
Adamts18 T A 8: 114,504,380 (GRCm39) Q80L possibly damaging Het
Apbb2 T A 5: 66,609,439 (GRCm39) K69N probably damaging Het
Ascc3 C T 10: 50,718,279 (GRCm39) R1991* probably null Het
BC035947 T A 1: 78,474,960 (GRCm39) N524I probably damaging Het
Bpifa1 A G 2: 153,985,796 (GRCm39) N37S unknown Het
Cfap91 T A 16: 38,152,604 (GRCm39) D202V probably damaging Het
Crnkl1 A T 2: 145,760,473 (GRCm39) D648E probably benign Het
Cul5 C A 9: 53,569,973 (GRCm39) G86V probably benign Het
Cyfip1 A C 7: 55,576,061 (GRCm39) D1077A probably damaging Het
Dennd4a T C 9: 64,804,011 (GRCm39) S1117P probably benign Het
Dnaaf8 T C 16: 4,791,932 (GRCm39) noncoding transcript Het
Elmo2 A T 2: 165,136,192 (GRCm39) M618K possibly damaging Het
Fggy A G 4: 95,585,225 (GRCm39) T35A probably damaging Het
Gad2 G A 2: 22,575,079 (GRCm39) probably null Het
Gtf3c2 A C 5: 31,325,425 (GRCm39) F455V possibly damaging Het
H4c16 C T 6: 136,781,292 (GRCm39) G29D probably damaging Het
Hacl1 C A 14: 31,341,873 (GRCm39) A311S probably damaging Het
Kat6b G A 14: 21,684,547 (GRCm39) D611N probably damaging Het
Kifap3 T C 1: 163,693,041 (GRCm39) I611T probably damaging Het
Lrba A G 3: 86,226,911 (GRCm39) Y683C probably damaging Het
Mfsd14a T C 3: 116,427,399 (GRCm39) N413S probably benign Het
Mtmr11 T A 3: 96,078,518 (GRCm39) D691E possibly damaging Het
Mzf1 A T 7: 12,787,116 (GRCm39) F64I probably benign Het
Neu2 G T 1: 87,524,478 (GRCm39) Q154H probably damaging Het
Nod1 C A 6: 54,916,312 (GRCm39) K128N probably damaging Het
Noxred1 T A 12: 87,270,976 (GRCm39) Q215L possibly damaging Het
Npat A G 9: 53,481,424 (GRCm39) E1044G probably damaging Het
Npr1 A G 3: 90,366,800 (GRCm39) probably benign Het
Pdcd6 T C 13: 74,452,133 (GRCm39) D169G probably damaging Het
Pld3 G T 7: 27,237,093 (GRCm39) T262N probably benign Het
Plxna1 T C 6: 89,299,704 (GRCm39) probably benign Het
Prh1 A G 6: 132,549,174 (GRCm39) Q227R unknown Het
Prtg C A 9: 72,716,999 (GRCm39) Y113* probably null Het
Rbm27 T A 18: 42,433,450 (GRCm39) V242E possibly damaging Het
Ripor1 T C 8: 106,342,636 (GRCm39) L198P probably damaging Het
Rnpc3 T C 3: 113,410,360 (GRCm39) probably null Het
Serpinf2 T C 11: 75,324,065 (GRCm39) T321A probably benign Het
Sh3gl1 T C 17: 56,326,119 (GRCm39) D129G probably damaging Het
Slc12a2 C A 18: 58,077,068 (GRCm39) P1189Q probably damaging Het
Slc16a9 T C 10: 70,118,320 (GRCm39) M213T probably benign Het
Spata31f3 A T 4: 42,871,711 (GRCm39) D221E probably damaging Het
Svil G A 18: 5,056,854 (GRCm39) probably null Het
Synpo A G 18: 60,737,118 (GRCm39) L37P probably damaging Het
Tmprss9 A G 10: 80,718,580 (GRCm39) H87R probably benign Het
Tmtc1 A T 6: 148,139,353 (GRCm39) L885Q probably damaging Het
Ttc41 T C 10: 86,586,128 (GRCm39) S811P possibly damaging Het
Vmn2r23 T C 6: 123,689,901 (GRCm39) V259A probably benign Het
Wwox T A 8: 115,406,586 (GRCm39) H192Q probably benign 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
R0413:Nid1 UTSW 13 13,656,681 (GRCm39) missense probably benign 0.01
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
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'- TTGGAAGGATAGCTGCCTGC -3'
(R):5'- AGGTCCCACATGAGGACAAC -3'

Sequencing Primer
(F):5'- AAGGCACACATTCATTTCTTTGTTC -3'
(R):5'- CCATCCAAGAAAATGCATAGTTCCAG -3'
Posted On 2017-02-10