Incidental Mutation 'R1462:Tfam'
ID 158965
Institutional Source Beutler Lab
Gene Symbol Tfam
Ensembl Gene ENSMUSG00000003923
Gene Name transcription factor A, mitochondrial
Synonyms Hmgts, tsHMG, mtTFA
MMRRC Submission 039516-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1462 (G1)
Quality Score 225
Status Not validated
Chromosome 10
Chromosomal Location 71061294-71074110 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 71071380 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 94 (E94G)
Ref Sequence ENSEMBL: ENSMUSP00000090086 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000092430] [ENSMUST00000105432] [ENSMUST00000121685] [ENSMUST00000152505]
AlphaFold P40630
Predicted Effect probably damaging
Transcript: ENSMUST00000092430
AA Change: E94G

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000090086
Gene: ENSMUSG00000003923
AA Change: E94G

DomainStartEndE-ValueType
HMG 48 118 4.91e-21 SMART
low complexity region 129 148 N/A INTRINSIC
HMG 153 219 4.66e-13 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000105432
AA Change: E66G

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000101072
Gene: ENSMUSG00000003923
AA Change: E66G

DomainStartEndE-ValueType
HMG 20 90 4.91e-21 SMART
low complexity region 101 120 N/A INTRINSIC
HMG 125 191 4.66e-13 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000121685
AA Change: E50G

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000113581
Gene: ENSMUSG00000003923
AA Change: E50G

DomainStartEndE-ValueType
HMG 4 74 4.91e-21 SMART
low complexity region 85 104 N/A INTRINSIC
HMG 109 175 4.66e-13 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000145220
Predicted Effect probably damaging
Transcript: ENSMUST00000152505
AA Change: E50G

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000120871
Gene: ENSMUSG00000003923
AA Change: E50G

DomainStartEndE-ValueType
HMG 4 74 4.91e-21 SMART
low complexity region 85 104 N/A INTRINSIC
Blast:HMG 109 143 6e-16 BLAST
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 98.7%
  • 3x: 97.4%
  • 10x: 92.6%
  • 20x: 79.9%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a key mitochondrial transcription factor containing two high mobility group motifs. The encoded protein also functions in mitochondrial DNA replication and repair. Sequence polymorphisms in this gene are associated with Alzheimer's and Parkinson's diseases. There are pseudogenes for this gene on chromosomes 6, 7, and 11. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]
PHENOTYPE: Homozygous null mutants exhibit retarded growth, abnormal somite development, lack of optic discs, cardiac defects and delayed neural development. Mutants die by embryonic day 10.5. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930433I11Rik C A 7: 40,642,370 (GRCm39) S104* probably null Het
Abca9 T C 11: 110,051,342 (GRCm39) D118G probably benign Het
Adamts16 A G 13: 70,984,253 (GRCm39) F137L probably benign Het
Adamts3 T C 5: 90,009,208 (GRCm39) I152V probably benign Het
Adcy4 T A 14: 56,015,765 (GRCm39) E441D possibly damaging Het
Adgra1 T A 7: 139,455,745 (GRCm39) Y458N probably damaging Het
Bhlhe22 C G 3: 18,109,946 (GRCm39) S332C probably damaging Het
Card19 T A 13: 49,358,760 (GRCm39) Q71L probably benign Het
Ccdc12 T C 9: 110,485,662 (GRCm39) L11P probably damaging Het
Cdadc1 A G 14: 59,813,307 (GRCm39) Y367H probably damaging Het
Cdc5l G T 17: 45,719,288 (GRCm39) Q542K possibly damaging Het
Cep170 T C 1: 176,584,211 (GRCm39) K723E possibly damaging Het
Cep70 A G 9: 99,145,773 (GRCm39) I147V probably benign Het
Cfap58 A T 19: 47,950,869 (GRCm39) H410L probably damaging Het
Chat T C 14: 32,142,735 (GRCm39) K418R probably damaging Het
Cic T G 7: 24,971,032 (GRCm39) D254E probably damaging Het
Ckap4 T C 10: 84,363,431 (GRCm39) E544G probably damaging Het
Crnkl1 C T 2: 145,763,739 (GRCm39) A500T probably damaging Het
Cyp2c38 T C 19: 39,380,632 (GRCm39) N418D probably damaging Het
Daam1 A T 12: 71,990,916 (GRCm39) I177L unknown Het
Ercc5 A G 1: 44,219,784 (GRCm39) T1019A probably damaging Het
F13b T A 1: 139,435,374 (GRCm39) V173E probably damaging Het
Fam20a A C 11: 109,568,143 (GRCm39) F316V probably damaging Het
Flrt2 T C 12: 95,746,112 (GRCm39) V150A probably damaging Het
Fnta A C 8: 26,489,599 (GRCm39) probably null Het
Ghsr A G 3: 27,426,025 (GRCm39) D27G probably benign Het
Gtpbp1 A G 15: 79,592,086 (GRCm39) N96D probably damaging Het
H1f7 A T 15: 98,154,454 (GRCm39) W232R unknown Het
Ibtk A T 9: 85,606,198 (GRCm39) I443N probably damaging Het
Ifi207 T C 1: 173,552,513 (GRCm39) H968R probably damaging Het
Ifit2 A G 19: 34,550,586 (GRCm39) D42G probably null Het
Il17rc A T 6: 113,455,950 (GRCm39) D265V probably damaging Het
Itfg2 T C 6: 128,401,691 (GRCm39) D29G probably damaging Het
Itprid1 A G 6: 55,952,649 (GRCm39) H864R probably damaging Het
Lrrc1 A G 9: 77,349,547 (GRCm39) F295L probably benign Het
Mrps28 T A 3: 8,965,184 (GRCm39) H85L possibly damaging Het
Mtpn T A 6: 35,499,693 (GRCm39) K37M possibly damaging Het
Mug1 C T 6: 121,859,588 (GRCm39) H1196Y probably benign Het
Mup4 T C 4: 59,960,084 (GRCm39) H60R possibly damaging Het
Mybl2 T C 2: 162,914,628 (GRCm39) S249P probably benign Het
Naip6 A G 13: 100,436,748 (GRCm39) Y592H possibly damaging Het
Nrp1 A G 8: 129,229,279 (GRCm39) N919S probably benign Het
Nudt9 C T 5: 104,212,904 (GRCm39) Q326* probably null Het
Or5w13 A T 2: 87,523,720 (GRCm39) C169S probably damaging Het
Or6c76b A G 10: 129,693,100 (GRCm39) T238A probably damaging Het
Or7g17 T A 9: 18,768,407 (GRCm39) M162K probably benign Het
Or9k7 T A 10: 130,046,592 (GRCm39) I136F probably benign Het
Pcsk4 T C 10: 80,161,815 (GRCm39) E142G probably damaging Het
Pde3a C A 6: 141,405,560 (GRCm39) P471T probably benign Het
Pign A T 1: 105,512,727 (GRCm39) V652E possibly damaging Het
Prkcb T A 7: 122,181,672 (GRCm39) M420K probably damaging Het
Prr14 T A 7: 127,073,160 (GRCm39) probably null Het
Rchy1 T A 5: 92,105,741 (GRCm39) Q69L probably damaging Het
Sec23ip T G 7: 128,367,862 (GRCm39) S625A probably benign Het
Smpdl3b A G 4: 132,473,925 (GRCm39) S47P probably damaging Het
Speer4a3 T A 5: 26,156,623 (GRCm39) I119F possibly damaging Het
Stil G A 4: 114,881,161 (GRCm39) M568I probably benign Het
Syt3 T A 7: 44,045,434 (GRCm39) V558E probably damaging Het
Szt2 A G 4: 118,231,164 (GRCm39) V2533A unknown Het
Tenm4 A G 7: 96,353,360 (GRCm39) Y384C probably damaging Het
Tmbim7 A G 5: 3,714,304 (GRCm39) T14A probably damaging Het
Tmtc2 A T 10: 105,409,566 (GRCm39) Y15* probably null Het
Uhrf1 C T 17: 56,625,035 (GRCm39) A526V probably damaging Het
Vmn2r67 T C 7: 84,805,046 (GRCm39) D22G probably benign Het
Vmn2r96 A G 17: 18,817,660 (GRCm39) I412M possibly damaging Het
Wdr17 A T 8: 55,123,363 (GRCm39) I479K probably damaging Het
Wt1 T C 2: 104,997,176 (GRCm39) V371A probably damaging Het
Zfp536 G T 7: 37,178,735 (GRCm39) S226Y probably damaging Het
Zfp827 T C 8: 79,803,108 (GRCm39) V560A probably benign Het
Other mutations in Tfam
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01773:Tfam APN 10 71,072,805 (GRCm39) missense possibly damaging 0.56
PIT4142001:Tfam UTSW 10 71,070,813 (GRCm39) missense possibly damaging 0.88
R1462:Tfam UTSW 10 71,071,380 (GRCm39) missense probably damaging 1.00
R4367:Tfam UTSW 10 71,069,233 (GRCm39) missense probably damaging 1.00
R4675:Tfam UTSW 10 71,069,225 (GRCm39) missense probably benign 0.22
R4684:Tfam UTSW 10 71,073,677 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- AGCAACTGGCCTTCATTCCTGAC -3'
(R):5'- ACTCTAGCAGTGGGTTTCCAAGGAC -3'

Sequencing Primer
(F):5'- ATTACCTGTGTGGACAGGACC -3'
(R):5'- GGTTTTGGTAATCTACAACATACTCC -3'
Posted On 2014-03-14