Incidental Mutation 'R6615:Nipa1'
ID 523940
Institutional Source Beutler Lab
Gene Symbol Nipa1
Ensembl Gene ENSMUSG00000047037
Gene Name non imprinted in Prader-Willi/Angelman syndrome 1 homolog (human)
Synonyms 1110027G09Rik, A830014A18Rik, Spg6
MMRRC Submission 044738-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6615 (G1)
Quality Score 208.009
Status Validated
Chromosome 7
Chromosomal Location 55628232-55669348 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 55629571 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Tyrosine at position 181 (N181Y)
Ref Sequence ENSEMBL: ENSMUSP00000053871 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000052204]
AlphaFold Q8BHK1
Predicted Effect probably damaging
Transcript: ENSMUST00000052204
AA Change: N181Y

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000053871
Gene: ENSMUSG00000047037
AA Change: N181Y

DomainStartEndE-ValueType
Pfam:Mg_trans_NIPA 21 308 1.6e-86 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130189
Predicted Effect noncoding transcript
Transcript: ENSMUST00000154016
Predicted Effect noncoding transcript
Transcript: ENSMUST00000205400
Meta Mutation Damage Score 0.2821 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.0%
  • 20x: 94.4%
Validation Efficiency 100% (51/51)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a magnesium transporter that associates with early endosomes and the cell surface in a variety of neuronal and epithelial cells. This protein may play a role in nervous system development and maintenance. Multiple transcript variants encoding different isoforms have been found for this gene. Mutations in this gene have been associated with autosomal dominant spastic paraplegia 6. [provided by RefSeq, Nov 2008]
Allele List at MGI
Other mutations in this stock
Total: 50 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Avl9 T C 6: 56,730,870 (GRCm39) V598A probably benign Het
Bcar3 T A 3: 122,220,282 (GRCm39) S60T probably benign Het
Bean1 CT C 8: 104,908,664 (GRCm39) probably null Homo
Calm3 A G 7: 16,651,508 (GRCm39) probably null Het
Ccdc113 A C 8: 96,272,620 (GRCm39) E242D probably benign Het
Celsr1 C T 15: 85,786,315 (GRCm39) probably null Het
Clhc1 T A 11: 29,528,149 (GRCm39) M559K possibly damaging Het
Dhx36 T A 3: 62,396,338 (GRCm39) I440L probably benign Het
Dnah7c A T 1: 46,554,599 (GRCm39) T445S probably benign Het
Dnah7c A G 1: 46,688,511 (GRCm39) S1894G probably benign Het
Dnah7c C A 1: 46,688,500 (GRCm39) T1890K probably benign Het
Dsc2 T A 18: 20,165,576 (GRCm39) H843L possibly damaging Het
F11 T C 8: 45,701,811 (GRCm39) Y333C probably benign Het
Fbxo41 T C 6: 85,455,505 (GRCm39) T560A possibly damaging Het
Fbxo7 A T 10: 85,880,398 (GRCm39) H282L possibly damaging Het
Gmnc T G 16: 26,779,278 (GRCm39) D243A probably benign Het
Hdac5 C A 11: 102,087,882 (GRCm39) probably null Het
Krt87 A G 15: 101,334,443 (GRCm39) V188A probably benign Het
Lpxn G A 19: 12,802,163 (GRCm39) V163M probably benign Het
Lrrk1 A T 7: 65,931,396 (GRCm39) L55Q probably damaging Het
Ltbp2 C T 12: 84,860,091 (GRCm39) C621Y probably damaging Het
Marchf8 A G 6: 116,382,624 (GRCm39) E147G probably damaging Het
Muc16 T G 9: 18,558,484 (GRCm39) H2603P unknown Het
Nt5el T A 13: 105,248,993 (GRCm39) N402K probably damaging Het
Or14c45 A G 7: 86,176,120 (GRCm39) T52A probably benign Het
Or2h2c G A 17: 37,422,494 (GRCm39) P127S probably damaging Het
Or4k37 A G 2: 111,159,457 (GRCm39) D231G probably benign Het
Or51f23c-ps1 T C 7: 102,430,994 (GRCm39) F104L probably damaging Het
Or7g35 A G 9: 19,496,285 (GRCm39) I151V probably benign Het
Pcf11 T A 7: 92,307,090 (GRCm39) Q1026L probably damaging Het
Ptch1 T G 13: 63,687,644 (GRCm39) K378T possibly damaging Het
Ptprm C T 17: 67,660,951 (GRCm39) probably null Het
Pxmp2 C A 5: 110,425,573 (GRCm39) W154L possibly damaging Het
Rdh7 T G 10: 127,720,491 (GRCm39) S294R probably damaging Het
Rexo1 C T 10: 80,379,848 (GRCm39) R994Q possibly damaging Het
Sacs A G 14: 61,446,383 (GRCm39) T2810A probably benign Het
Serpina3c A T 12: 104,117,980 (GRCm39) H119Q possibly damaging Het
Slc12a2 T G 18: 58,031,200 (GRCm39) I335R probably damaging Het
Slc25a13 C T 6: 6,073,454 (GRCm39) R468Q probably damaging Het
Slc5a6 C T 5: 31,194,174 (GRCm39) V628I probably benign Het
Srsf2 T C 11: 116,743,905 (GRCm39) probably null Het
Sugp2 A G 8: 70,695,420 (GRCm39) Q131R possibly damaging Het
Syne1 T C 10: 5,251,340 (GRCm39) R2525G probably damaging Het
Tars3 T C 7: 65,327,890 (GRCm39) F533S probably damaging Het
Tmem8b G T 4: 43,682,249 (GRCm39) G82W probably damaging Het
Unc13c A G 9: 73,837,890 (GRCm39) I987T possibly damaging Het
Usp44 T C 10: 93,682,351 (GRCm39) V267A possibly damaging Het
Wac C A 18: 7,868,884 (GRCm39) probably null Het
Xkr5 T C 8: 18,983,569 (GRCm39) I658V probably benign Het
Zbtb38 A T 9: 96,568,707 (GRCm39) Y792* probably null Het
Other mutations in Nipa1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01327:Nipa1 APN 7 55,629,409 (GRCm39) missense probably benign 0.20
impressionless UTSW 7 55,629,354 (GRCm39) missense probably benign 0.04
untouched UTSW 7 55,629,571 (GRCm39) missense probably damaging 1.00
R2116:Nipa1 UTSW 7 55,635,273 (GRCm39) missense possibly damaging 0.69
R2141:Nipa1 UTSW 7 55,647,259 (GRCm39) splice site probably null
R2142:Nipa1 UTSW 7 55,647,259 (GRCm39) splice site probably null
R4823:Nipa1 UTSW 7 55,629,436 (GRCm39) missense possibly damaging 0.71
R5424:Nipa1 UTSW 7 55,629,223 (GRCm39) missense possibly damaging 0.90
R5463:Nipa1 UTSW 7 55,629,205 (GRCm39) nonsense probably null
R6459:Nipa1 UTSW 7 55,629,354 (GRCm39) missense probably benign 0.04
R6468:Nipa1 UTSW 7 55,669,252 (GRCm39) missense probably benign 0.39
R7662:Nipa1 UTSW 7 55,629,372 (GRCm39) missense probably damaging 0.98
R7921:Nipa1 UTSW 7 55,629,558 (GRCm39) missense probably damaging 1.00
R7957:Nipa1 UTSW 7 55,629,547 (GRCm39) missense probably damaging 1.00
R8445:Nipa1 UTSW 7 55,629,466 (GRCm39) missense probably benign 0.03
X0064:Nipa1 UTSW 7 55,629,507 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TTGGACAATGATGCTGCAGC -3'
(R):5'- TACCCTTGTGGCTGCAGTAG -3'

Sequencing Primer
(F):5'- AATGATGCTGCAGCCCAGG -3'
(R):5'- TTGGGCAAGTGCTCTACCACTAAG -3'
Posted On 2018-06-22