Incidental Mutation 'R6459:Nipa1'
ID 517513
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 044594-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6459 (G1)
Quality Score 176.009
Status Validated
Chromosome 7
Chromosomal Location 55628232-55669348 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 55629354 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 253 (V253A)
Ref Sequence ENSEMBL: ENSMUSP00000053871 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000052204]
AlphaFold Q8BHK1
Predicted Effect probably benign
Transcript: ENSMUST00000052204
AA Change: V253A

PolyPhen 2 Score 0.042 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000053871
Gene: ENSMUSG00000047037
AA Change: V253A

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 0.0809 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 97.9%
  • 20x: 93.6%
Validation Efficiency 98% (52/53)
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: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abr C A 11: 76,315,815 (GRCm39) R583L probably damaging Het
Acss1 A G 2: 150,509,840 (GRCm39) I93T probably damaging Het
Ank3 C T 10: 69,827,577 (GRCm39) probably benign Het
Aoah A G 13: 21,184,112 (GRCm39) Y392C probably damaging Het
Atl3 A T 19: 7,498,163 (GRCm39) E186D probably benign Het
Atp4a A G 7: 30,411,887 (GRCm39) K41E probably benign Het
Atp9a G A 2: 168,509,933 (GRCm39) P500L probably damaging Het
Ccdc88b A T 19: 6,832,246 (GRCm39) V363D possibly damaging Het
Cftr T C 6: 18,258,235 (GRCm39) V532A probably damaging Het
Cldn13 T C 5: 134,943,769 (GRCm39) T139A possibly damaging Het
Cnksr3 T C 10: 7,076,820 (GRCm39) Y124C probably benign Het
Cyb5r2 T C 7: 107,352,462 (GRCm39) K161E possibly damaging Het
Epop T C 11: 97,519,333 (GRCm39) S259G possibly damaging Het
Fhl2 G A 1: 43,162,813 (GRCm39) T234I possibly damaging Het
Fnip2 T C 3: 79,388,941 (GRCm39) T567A possibly damaging Het
Frmd4b A G 6: 97,464,601 (GRCm39) C39R probably damaging Het
Grhl3 T C 4: 135,284,744 (GRCm39) N116S possibly damaging Het
Igkv14-111 A T 6: 68,233,725 (GRCm39) R75S probably benign Het
Il16 A T 7: 83,371,529 (GRCm39) D92E probably damaging Het
Il16 C A 7: 83,371,536 (GRCm39) G90V probably damaging Het
Ipo11 T C 13: 107,002,277 (GRCm39) probably null Het
Kng2 A G 16: 22,830,865 (GRCm39) I148T probably damaging Het
Lrrc41 T C 4: 115,945,977 (GRCm39) S231P possibly damaging Het
Maneal C T 4: 124,750,635 (GRCm39) V374I possibly damaging Het
Mgat4c T A 10: 102,220,988 (GRCm39) L90Q probably damaging Het
Mrps28 A G 3: 8,965,040 (GRCm39) probably null Het
Ncapd3 A G 9: 26,963,051 (GRCm39) D452G probably benign Het
Nefh T C 11: 4,889,551 (GRCm39) T1023A unknown Het
Or5ac17 C T 16: 59,036,383 (GRCm39) V198M probably benign Het
Or5b97 G T 19: 12,878,369 (GRCm39) F258L possibly damaging Het
Or5m11 G T 2: 85,781,862 (GRCm39) G152C probably damaging Het
Or8d23 A G 9: 38,841,961 (GRCm39) S165G probably benign Het
Or8k41 T A 2: 86,313,573 (GRCm39) H171L probably benign Het
Pak1 A G 7: 97,557,088 (GRCm39) D495G probably benign Het
Pcm1 G A 8: 41,714,073 (GRCm39) R213H probably damaging Het
Prg4 T C 1: 150,330,052 (GRCm39) probably benign Het
Proser1 C T 3: 53,385,750 (GRCm39) T544M possibly damaging Het
Rftn1 T C 17: 50,354,334 (GRCm39) M343V probably benign Het
Ryr1 T C 7: 28,715,079 (GRCm39) I4656V probably benign Het
Scg2 T A 1: 79,414,007 (GRCm39) N239Y probably damaging Het
Sec16a C A 2: 26,313,512 (GRCm39) M1949I probably benign Het
Sipa1l2 A G 8: 126,171,223 (GRCm39) probably null Het
Slc10a2 A C 8: 5,148,581 (GRCm39) probably null Het
Slc25a16 C T 10: 62,773,256 (GRCm39) Q164* probably null Het
Specc1l T C 10: 75,082,001 (GRCm39) Y483H probably damaging Het
Ston1 T C 17: 88,943,896 (GRCm39) V434A probably benign Het
Tarbp2 A G 15: 102,426,914 (GRCm39) probably benign Het
Trappc8 C T 18: 20,969,925 (GRCm39) V1022M probably benign Het
Tsen54 T C 11: 115,712,506 (GRCm39) V269A probably damaging Het
Vps13a A T 19: 16,641,382 (GRCm39) M78K possibly damaging Het
Vwa5b2 A G 16: 20,413,429 (GRCm39) T215A probably damaging Het
Zc3h7a A G 16: 10,971,025 (GRCm39) Y335H probably damaging Het
Zfp994 T A 17: 22,419,527 (GRCm39) Q474L possibly damaging 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
R6468:Nipa1 UTSW 7 55,669,252 (GRCm39) missense probably benign 0.39
R6615:Nipa1 UTSW 7 55,629,571 (GRCm39) missense probably damaging 1.00
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'- ACCCCTTGGTTGCATCTTAG -3'
(R):5'- GGAGTTTCACTGTGCCTTCC -3'

Sequencing Primer
(F):5'- TCATCTCTCCAAGGTTGAAGTTG -3'
(R):5'- ACTGTGCCTTCCACCAAG -3'
Posted On 2018-05-21