Incidental Mutation 'R3709:Idh3a'
ID 259494
Institutional Source Beutler Lab
Gene Symbol Idh3a
Ensembl Gene ENSMUSG00000032279
Gene Name isocitrate dehydrogenase 3 (NAD+) alpha
Synonyms 1500012E04Rik
MMRRC Submission 040702-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.968) question?
Stock # R3709 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 54493795-54511946 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 54493810 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 4 (S4P)
Ref Sequence ENSEMBL: ENSMUSP00000149036 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000167866] [ENSMUST00000215273] [ENSMUST00000217484]
AlphaFold Q9D6R2
Predicted Effect probably benign
Transcript: ENSMUST00000167866
AA Change: S4P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000127526
Gene: ENSMUSG00000032279
AA Change: S4P

DomainStartEndE-ValueType
Iso_dh 33 358 1.37e-169 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000213729
Predicted Effect possibly damaging
Transcript: ENSMUST00000215273
AA Change: S4P

PolyPhen 2 Score 0.827 (Sensitivity: 0.84; Specificity: 0.93)
Predicted Effect probably benign
Transcript: ENSMUST00000217484
AA Change: S22P

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
Meta Mutation Damage Score 0.1795 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 93.9%
Validation Efficiency 98% (50/51)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Isocitrate dehydrogenases catalyze the oxidative decarboxylation of isocitrate to 2-oxoglutarate. These enzymes belong to two distinct subclasses, one of which utilizes NAD(+) as the electron acceptor and the other NADP(+). Five isocitrate dehydrogenases have been reported: three NAD(+)-dependent isocitrate dehydrogenases, which localize to the mitochondrial matrix, and two NADP(+)-dependent isocitrate dehydrogenases, one of which is mitochondrial and the other predominantly cytosolic. NAD(+)-dependent isocitrate dehydrogenases catalyze the allosterically regulated rate-limiting step of the tricarboxylic acid cycle. Each isozyme is a heterotetramer that is composed of two alpha subunits, one beta subunit, and one gamma subunit. The protein encoded by this gene is the alpha subunit of one isozyme of NAD(+)-dependent isocitrate dehydrogenase. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for an ENU-induced mutation exhibit progressive retinal degeneration and decreased visual acuity. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 50 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9930111J21Rik2 T G 11: 48,910,480 (GRCm39) D651A probably damaging Het
Abcb1a A G 5: 8,788,738 (GRCm39) N1039S probably benign Het
Abcc2 G T 19: 43,786,885 (GRCm39) V169F possibly damaging Het
Adcy8 T C 15: 64,597,384 (GRCm39) probably benign Het
Aida C A 1: 183,085,610 (GRCm39) probably null Het
Armc8 A G 9: 99,402,550 (GRCm39) I333T probably damaging Het
B4galt3 C A 1: 171,101,613 (GRCm39) H196N probably damaging Het
Ccdc92b C A 11: 74,528,933 (GRCm39) R146S probably damaging Het
Cdc42bpa A G 1: 179,892,628 (GRCm39) D264G probably damaging Het
Cenpf A G 1: 189,381,009 (GRCm39) S2804P possibly damaging Het
Cic A G 7: 24,986,406 (GRCm39) D1276G probably damaging Het
Cldn19 T C 4: 119,114,094 (GRCm39) S79P possibly damaging Het
Ctdp1 G A 18: 80,493,428 (GRCm39) Q356* probably null Het
Cyp2c69 A G 19: 39,839,667 (GRCm39) probably benign Het
Dhrs3 T C 4: 144,620,281 (GRCm39) probably null Het
Fhod3 T A 18: 25,223,815 (GRCm39) W1054R probably damaging Het
Gfral G A 9: 76,100,725 (GRCm39) R238* probably null Het
Gm10322 C A 10: 59,451,941 (GRCm39) D19E possibly damaging Het
Gprc6a CAAA CA 10: 51,491,776 (GRCm39) probably null Het
Il15ra G T 2: 11,735,458 (GRCm39) probably null Het
Ipo8 A T 6: 148,707,842 (GRCm39) probably null Het
Iqgap1 G A 7: 80,366,835 (GRCm39) T1595I possibly damaging Het
Kalrn C T 16: 34,212,400 (GRCm39) probably null Het
Klrb1a T C 6: 128,595,466 (GRCm39) D96G probably benign Het
Lrp1b C T 2: 40,587,454 (GRCm39) V165M unknown Het
Lrp4 A C 2: 91,320,811 (GRCm39) T975P possibly damaging Het
Lsm14a T A 7: 34,053,204 (GRCm39) I283F probably damaging Het
Mael T C 1: 166,066,135 (GRCm39) D34G probably damaging Het
Map2 C T 1: 66,455,015 (GRCm39) Q1302* probably null Het
Mctp1 T C 13: 76,972,999 (GRCm39) probably null Het
Mlxip T C 5: 123,585,537 (GRCm39) V642A probably benign Het
Myh9 T C 15: 77,657,547 (GRCm39) E1066G possibly damaging Het
Naa35 T A 13: 59,765,846 (GRCm39) probably benign Het
Nacc1 T A 8: 85,403,828 (GRCm39) I16F probably damaging Het
Ncapd3 T A 9: 26,963,645 (GRCm39) N499K probably benign Het
Or10ab4 A G 7: 107,655,004 (GRCm39) M272V possibly damaging Het
Osbpl10 C A 9: 115,036,655 (GRCm39) P253Q probably benign Het
Ptpn21 G T 12: 98,654,800 (GRCm39) S722R probably benign Het
Rab44 C T 17: 29,358,843 (GRCm39) P344S probably benign Het
Rbms2 C T 10: 127,979,312 (GRCm39) R139Q probably damaging Het
Sh3bp2 T C 5: 34,709,002 (GRCm39) Y32H probably damaging Het
Slc6a15 A G 10: 103,229,275 (GRCm39) I105V probably benign Het
Thumpd3 A G 6: 113,032,652 (GRCm39) D130G possibly damaging Het
Trib1 A G 15: 59,526,210 (GRCm39) Y260C probably damaging Het
Tsks G T 7: 44,601,309 (GRCm39) R208L possibly damaging Het
Ttn G T 2: 76,577,585 (GRCm39) S22690* probably null Het
Ttyh2 T G 11: 114,609,958 (GRCm39) S510A possibly damaging Het
Was G T X: 7,952,927 (GRCm39) S271R probably benign Het
Zfp267 T A 3: 36,213,725 (GRCm39) C20S possibly damaging Het
Zfp472 T A 17: 33,196,685 (GRCm39) Y253* probably null Het
Other mutations in Idh3a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01534:Idh3a APN 9 54,508,506 (GRCm39) splice site probably benign
IGL02547:Idh3a APN 9 54,499,679 (GRCm39) missense probably benign 0.00
IGL02593:Idh3a APN 9 54,503,477 (GRCm39) splice site probably benign
IGL03408:Idh3a APN 9 54,504,206 (GRCm39) missense probably benign 0.00
ANU23:Idh3a UTSW 9 54,493,829 (GRCm39) critical splice donor site probably null
R2496:Idh3a UTSW 9 54,510,633 (GRCm39) missense probably benign 0.20
R3877:Idh3a UTSW 9 54,499,679 (GRCm39) missense probably benign 0.00
R4962:Idh3a UTSW 9 54,503,325 (GRCm39) missense possibly damaging 0.86
R6054:Idh3a UTSW 9 54,493,829 (GRCm39) critical splice donor site probably null
R7246:Idh3a UTSW 9 54,499,756 (GRCm39) missense probably damaging 1.00
R7426:Idh3a UTSW 9 54,508,492 (GRCm39) missense probably benign
R7450:Idh3a UTSW 9 54,503,367 (GRCm39) missense probably damaging 1.00
R7678:Idh3a UTSW 9 54,502,453 (GRCm39) missense probably damaging 1.00
R8491:Idh3a UTSW 9 54,506,963 (GRCm39) critical splice donor site probably null
R9121:Idh3a UTSW 9 54,493,829 (GRCm39) critical splice donor site probably null
R9654:Idh3a UTSW 9 54,497,182 (GRCm39) missense probably benign
Z1177:Idh3a UTSW 9 54,503,433 (GRCm39) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- CGCGCGTCATCAAAAGATG -3'
(R):5'- TTTACCCGGTCAAAGGCTGAG -3'

Sequencing Primer
(F):5'- ATTGGTCAGCTAGCGGCAG -3'
(R):5'- TGTGCACCTATCCTGGAGG -3'
Posted On 2015-01-23