Incidental Mutation 'R2906:Gtf2a1l'
ID 477240
Institutional Source Beutler Lab
Gene Symbol Gtf2a1l
Ensembl Gene ENSMUSG00000024154
Gene Name general transcription factor IIA, 1-like
Synonyms Gtf2a1lf, 1700011N16Rik, Alf
MMRRC Submission 040493-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.650) question?
Stock # R2906 (G1)
Quality Score 225
Status Not validated
Chromosome 17
Chromosomal Location 88976088-89022580 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 89002083 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Histidine at position 313 (R313H)
Ref Sequence ENSEMBL: ENSMUSP00000024970 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000024970] [ENSMUST00000161481]
AlphaFold Q8R4I4
Predicted Effect possibly damaging
Transcript: ENSMUST00000024970
AA Change: R313H

PolyPhen 2 Score 0.922 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000024970
Gene: ENSMUSG00000024154
AA Change: R313H

DomainStartEndE-ValueType
TFIIA 9 468 6.87e-202 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000161481
SMART Domains Protein: ENSMUSP00000124286
Gene: ENSMUSG00000024154

DomainStartEndE-ValueType
Pfam:TFIIA 9 76 3.2e-29 PFAM
Pfam:TFIIA 70 243 3e-13 PFAM
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.2%
Validation Efficiency 97% (37/38)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The assembly and stability of the RNA polymerase II transcription pre-initiation complex on a eukaryotic core promoter involve the effects of transcription factor IIA (TFIIA) on the interaction between TATA-binding protein (TBP) and DNA. This gene encodes a germ cell-specific counterpart of the large (alpha/beta) subunit of general transcription factor TFIIA that is able to stabilize the binding of TBP to DNA and may be uniquely important to testis biology. Alternative splicing for this locus has been observed and two variants, encoding distinct isoforms, have been identified. Co-transcription of this gene and the neighboring upstream gene generates a rare transcript (SALF), which encodes a fusion protein comprised of sequence sharing identity with each individual gene product. [provided by RefSeq, Mar 2014]
Allele List at MGI
Other mutations in this stock
Total: 36 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam32 A T 8: 25,353,520 (GRCm39) W690R probably damaging Het
Adgrg6 A G 10: 14,308,694 (GRCm39) I800T probably benign Het
Afg3l2 G A 18: 67,573,292 (GRCm39) T170M probably damaging Het
Ap1b1 T A 11: 4,981,641 (GRCm39) N516K probably damaging Het
Armcx6 A T X: 133,650,199 (GRCm39) C211S probably damaging Het
Atp7b G A 8: 22,501,570 (GRCm39) T781I probably damaging Het
Cd96 T C 16: 45,871,850 (GRCm39) T432A possibly damaging Het
Col13a1 T C 10: 61,696,267 (GRCm39) probably benign Het
Ddx4 G T 13: 112,757,311 (GRCm39) probably benign Het
Dnm1l A T 16: 16,132,175 (GRCm39) S666T probably damaging Het
Duoxa1 C T 2: 122,135,155 (GRCm39) V197M probably benign Het
Gm6430 A T 1: 96,952,554 (GRCm39) noncoding transcript Het
Gucy2c A T 6: 136,685,385 (GRCm39) V852E probably damaging Het
Kcnk1 G T 8: 126,722,538 (GRCm39) V114L probably benign Het
Klra3 G T 6: 130,310,302 (GRCm39) Q73K probably damaging Het
Lax1 A T 1: 133,616,643 (GRCm39) M1K probably null Het
Lce1k T C 3: 92,713,882 (GRCm39) S101G unknown Het
Med12l T C 3: 59,164,503 (GRCm39) L1365P probably damaging Het
Mtx2 T C 2: 74,697,253 (GRCm39) S83P probably damaging Het
Naip2 A C 13: 100,298,504 (GRCm39) C511G probably damaging Het
Nefh A G 11: 4,890,216 (GRCm39) I801T probably benign Het
Or8g24 A G 9: 38,989,669 (GRCm39) V124A probably benign Het
Oxct2b A G 4: 123,010,823 (GRCm39) I248V probably benign Het
Pcdhgb2 A T 18: 37,823,908 (GRCm39) I300F probably damaging Het
Ptprc G A 1: 137,992,272 (GRCm39) A1285V possibly damaging Het
Rassf3 A G 10: 121,250,297 (GRCm39) L172P probably damaging Het
Rbm26 T A 14: 105,380,270 (GRCm39) T516S probably benign Het
Rpusd1 T C 17: 25,949,705 (GRCm39) S292P probably benign Het
Scamp5 A G 9: 57,351,146 (GRCm39) V172A probably damaging Het
Snx25 T C 8: 46,502,560 (GRCm39) probably null Het
Tmprss11g A G 5: 86,640,661 (GRCm39) probably benign Het
Ttll3 G C 6: 113,369,471 (GRCm39) probably benign Het
Uggt2 C T 14: 119,256,919 (GRCm39) S1105N probably benign Het
Usp45 T A 4: 21,834,338 (GRCm39) Y805* probably null Het
Zfp639 T C 3: 32,573,900 (GRCm39) L175P probably damaging Het
Zfp995 T C 17: 22,099,247 (GRCm39) D329G probably benign Het
Other mutations in Gtf2a1l
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00565:Gtf2a1l APN 17 89,001,723 (GRCm39) missense probably damaging 1.00
IGL00928:Gtf2a1l APN 17 89,001,890 (GRCm39) missense probably benign 0.09
IGL00974:Gtf2a1l APN 17 89,022,377 (GRCm39) missense probably damaging 1.00
IGL01024:Gtf2a1l APN 17 88,978,719 (GRCm39) missense probably damaging 1.00
IGL02429:Gtf2a1l APN 17 88,976,141 (GRCm39) start codon destroyed probably null 0.61
IGL02658:Gtf2a1l APN 17 88,976,146 (GRCm39) missense probably benign 0.01
IGL03377:Gtf2a1l APN 17 89,019,021 (GRCm39) missense probably benign 0.03
R0848:Gtf2a1l UTSW 17 89,001,657 (GRCm39) missense probably damaging 0.99
R0899:Gtf2a1l UTSW 17 88,976,152 (GRCm39) missense
R1435:Gtf2a1l UTSW 17 89,001,743 (GRCm39) missense probably damaging 1.00
R1716:Gtf2a1l UTSW 17 89,002,008 (GRCm39) missense probably benign 0.06
R1861:Gtf2a1l UTSW 17 89,022,382 (GRCm39) missense probably damaging 1.00
R2301:Gtf2a1l UTSW 17 89,018,900 (GRCm39) missense probably benign
R4281:Gtf2a1l UTSW 17 89,019,065 (GRCm39) missense possibly damaging 0.95
R4289:Gtf2a1l UTSW 17 89,001,884 (GRCm39) missense probably damaging 0.98
R4771:Gtf2a1l UTSW 17 88,997,448 (GRCm39) missense probably benign 0.23
R4904:Gtf2a1l UTSW 17 88,997,471 (GRCm39) critical splice donor site probably null
R4941:Gtf2a1l UTSW 17 89,022,350 (GRCm39) missense probably damaging 1.00
R5106:Gtf2a1l UTSW 17 89,002,073 (GRCm39) missense possibly damaging 0.95
R6003:Gtf2a1l UTSW 17 89,001,531 (GRCm39) missense probably damaging 1.00
R6035:Gtf2a1l UTSW 17 89,018,962 (GRCm39) missense probably benign 0.00
R6035:Gtf2a1l UTSW 17 89,018,962 (GRCm39) missense probably benign 0.00
R6128:Gtf2a1l UTSW 17 89,002,086 (GRCm39) missense probably null 0.94
R6246:Gtf2a1l UTSW 17 88,978,975 (GRCm39) missense probably benign 0.09
R6481:Gtf2a1l UTSW 17 89,019,053 (GRCm39) missense probably benign 0.09
R7344:Gtf2a1l UTSW 17 89,001,531 (GRCm39) missense probably damaging 1.00
R7462:Gtf2a1l UTSW 17 89,001,566 (GRCm39) missense possibly damaging 0.77
R8712:Gtf2a1l UTSW 17 89,022,351 (GRCm39) missense probably damaging 1.00
R8849:Gtf2a1l UTSW 17 89,001,566 (GRCm39) missense possibly damaging 0.77
R9178:Gtf2a1l UTSW 17 88,976,152 (GRCm39) missense
R9407:Gtf2a1l UTSW 17 89,001,531 (GRCm39) missense probably damaging 1.00
R9569:Gtf2a1l UTSW 17 89,001,948 (GRCm39) missense probably benign
R9760:Gtf2a1l UTSW 17 89,019,020 (GRCm39) missense probably benign 0.03
Predicted Primers
Posted On 2017-05-15