Incidental Mutation 'R7256:Gtf2h2'
ID 564294
Institutional Source Beutler Lab
Gene Symbol Gtf2h2
Ensembl Gene ENSMUSG00000021639
Gene Name general transcription factor II H, polypeptide 2
Synonyms Btf2p44, 44kDa, basal transcription factor 2, p44 subunit, p44
MMRRC Submission 045317-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R7256 (G1)
Quality Score 225.009
Status Validated
Chromosome 13
Chromosomal Location 100596726-100629087 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 100615709 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Isoleucine at position 271 (F271I)
Ref Sequence ENSEMBL: ENSMUSP00000065228 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000066984] [ENSMUST00000134842] [ENSMUST00000145266]
AlphaFold Q9JIB4
Predicted Effect probably benign
Transcript: ENSMUST00000066984
AA Change: F271I

PolyPhen 2 Score 0.052 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000065228
Gene: ENSMUSG00000021639
AA Change: F271I

DomainStartEndE-ValueType
VWA 58 240 1.02e-14 SMART
Blast:BIR 291 310 6e-7 BLAST
C1_4 345 388 3.13e-21 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000134842
SMART Domains Protein: ENSMUSP00000138748
Gene: ENSMUSG00000021639

DomainStartEndE-ValueType
Pfam:Ssl1 64 139 2.4e-27 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000145266
AA Change: F271I

PolyPhen 2 Score 0.063 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000138108
Gene: ENSMUSG00000021639
AA Change: F271I

DomainStartEndE-ValueType
VWA 58 240 1.02e-14 SMART
Blast:BIR 291 310 6e-7 BLAST
C1_4 345 388 3.13e-21 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000232450
Meta Mutation Damage Score 0.1159 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency 99% (70/71)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is part of a 500 kb inverted duplication on chromosome 5q13. This duplicated region contains at least four genes and repetitive elements which make it prone to rearrangements and deletions. The repetitiveness and complexity of the sequence have also caused difficulty in determining the organization of this genomic region. This gene is within the telomeric copy of the duplication. Deletion of this gene sometimes accompanies deletion of the neighboring SMN1 gene in spinal muscular atrophy (SMA) patients but it is unclear if deletion of this gene contributes to the SMA phenotype. This gene encodes the 44 kDa subunit of RNA polymerase II transcription initiation factor IIH which is involved in basal transcription and nucleotide excision repair. Transcript variants for this gene have been described, but their full length nature has not been determined. A second copy of this gene within the centromeric copy of the duplication has been described in the literature. It is reported to be different by either two or four base pairs; however, no sequence data is currently available for the centromeric copy of the gene. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamts5 A G 16: 85,659,923 (GRCm39) Y790H probably damaging Het
Bend3 A C 10: 43,369,667 (GRCm39) S7R probably benign Het
Ccdc106 A G 7: 5,063,325 (GRCm39) T277A probably damaging Het
Ccdc162 G A 10: 41,431,997 (GRCm39) A1832V probably damaging Het
Ccser1 A G 6: 61,288,851 (GRCm39) E338G probably benign Het
Cd86 CA CAA 16: 36,426,917 (GRCm39) probably null Het
Cecr2 T C 6: 120,739,490 (GRCm39) S1406P probably benign Het
Cep290 A G 10: 100,382,360 (GRCm39) T208A probably damaging Het
Cep85l A C 10: 53,172,351 (GRCm39) C569W probably damaging Het
Ces5a G A 8: 94,226,154 (GRCm39) T527I probably benign Het
Clca3a2 T A 3: 144,796,608 (GRCm39) I200F probably damaging Het
Cmas G A 6: 142,716,312 (GRCm39) D251N probably damaging Het
Ctcfl G T 2: 172,960,268 (GRCm39) A105E probably benign Het
Dclk2 C T 3: 86,700,566 (GRCm39) R638H probably damaging Het
Dctn6 A T 8: 34,557,962 (GRCm39) I170N probably damaging Het
Dnah2 T C 11: 69,321,920 (GRCm39) Y3800C probably damaging Het
Dsg2 G A 18: 20,724,988 (GRCm39) V465I possibly damaging Het
Dzip1 T C 14: 119,123,058 (GRCm39) T646A probably benign Het
Etv4 T A 11: 101,675,151 (GRCm39) probably null Het
Exoc3l2 T C 7: 19,218,628 (GRCm39) V549A unknown Het
Ficd G T 5: 113,876,880 (GRCm39) A352S probably damaging Het
Fry T G 5: 150,390,251 (GRCm39) I179S Het
Galntl5 A G 5: 25,400,298 (GRCm39) H109R probably benign Het
Garem1 C A 18: 21,281,811 (GRCm39) G182W probably damaging Het
Gm5916 A T 9: 36,032,285 (GRCm39) Y50N possibly damaging Het
Hivep2 G T 10: 14,004,845 (GRCm39) S481I probably benign Het
Homez T A 14: 55,094,877 (GRCm39) Q277L probably damaging Het
Hoxb4 C A 11: 96,210,722 (GRCm39) probably null Het
Igll1 A G 16: 16,678,957 (GRCm39) S118P probably damaging Het
Ikzf2 A C 1: 69,617,212 (GRCm39) probably null Het
Kif5b A G 18: 6,225,340 (GRCm39) V230A probably damaging Het
Ldlr T A 9: 21,657,040 (GRCm39) V719E probably benign Het
Lsm7 G A 10: 80,689,565 (GRCm39) R66W possibly damaging Het
Map3k13 T A 16: 21,710,988 (GRCm39) D90E probably benign Het
Mmrn1 A G 6: 60,953,098 (GRCm39) K460E probably damaging Het
Myh10 A C 11: 68,681,515 (GRCm39) N1061H probably damaging Het
Nepn A G 10: 52,277,089 (GRCm39) Q275R probably benign Het
Noc3l A T 19: 38,800,800 (GRCm39) D227E probably benign Het
Nploc4 G T 11: 120,319,376 (GRCm39) S61R probably benign Het
Nr4a2 T C 2: 57,002,381 (GRCm39) Y24C probably damaging Het
Nup160 T A 2: 90,553,699 (GRCm39) I1143N probably damaging Het
Or14a256 G T 7: 86,264,873 (GRCm39) H327N probably benign Het
Or4a15 A T 2: 89,192,838 (GRCm39) Y312N probably benign Het
Or8c17 T A 9: 38,180,004 (GRCm39) M57K probably damaging Het
Or8h7 A G 2: 86,720,956 (GRCm39) S188P probably damaging Het
Papola T A 12: 105,775,604 (GRCm39) C204S probably damaging Het
Peg10 CCACATCAGGATCCACATCAGGATGCACATCAGCATCAGGATCCCCATCAGGATGCACATCAGGATCCACATCAGGATGCACATCAG CCACATCAGGATCCACATCAGGATGCACATCAG 6: 4,756,398 (GRCm39) probably benign Het
Pgap1 A T 1: 54,532,366 (GRCm39) probably null Het
Pitrm1 A G 13: 6,606,633 (GRCm39) H229R probably damaging Het
Plcl1 A G 1: 55,737,377 (GRCm39) Q906R probably benign Het
Ppfia3 T C 7: 44,991,167 (GRCm39) N1018S probably benign Het
Pramel24 T A 4: 143,452,849 (GRCm39) D93E probably benign Het
Prkd1 A G 12: 50,435,125 (GRCm39) V534A possibly damaging Het
Pygm A T 19: 6,435,926 (GRCm39) I126F probably benign Het
Rag1 T C 2: 101,472,415 (GRCm39) Y909C probably damaging Het
Rasgrf2 G A 13: 92,032,637 (GRCm39) Q560* probably null Het
Rbp3 A T 14: 33,684,540 (GRCm39) I1190F possibly damaging Het
Reln T C 5: 22,183,921 (GRCm39) K1693E probably benign Het
Rgl2 T C 17: 34,153,964 (GRCm39) F457L possibly damaging Het
Rsph3a A G 17: 8,165,002 (GRCm39) T121A probably benign Het
Rufy3 A G 5: 88,762,806 (GRCm39) N112S possibly damaging Het
Ryr3 G A 2: 112,502,591 (GRCm39) Q3548* probably null Het
Sardh A T 2: 27,108,824 (GRCm39) V637D probably benign Het
Spata16 T C 3: 26,722,016 (GRCm39) V179A probably benign Het
Spopfm2 T C 3: 94,083,667 (GRCm39) E48G probably benign Het
Tbc1d30 G A 10: 121,124,870 (GRCm39) T319I probably damaging Het
Tlr2 T A 3: 83,744,913 (GRCm39) Q390L possibly damaging Het
Tmem53 C T 4: 117,109,237 (GRCm39) probably null Het
Vmn1r113 T A 7: 20,521,370 (GRCm39) I54N probably damaging Het
Vmn1r223 A C 13: 23,434,036 (GRCm39) Y210S probably damaging Het
Zbbx A T 3: 74,947,205 (GRCm39) H670Q probably benign Het
Other mutations in Gtf2h2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00585:Gtf2h2 APN 13 100,617,506 (GRCm39) unclassified probably benign
IGL00780:Gtf2h2 APN 13 100,615,729 (GRCm39) missense probably benign 0.01
IGL01475:Gtf2h2 APN 13 100,617,541 (GRCm39) missense probably damaging 1.00
IGL02298:Gtf2h2 APN 13 100,617,547 (GRCm39) missense probably damaging 1.00
IGL02754:Gtf2h2 APN 13 100,617,747 (GRCm39) missense probably damaging 1.00
R0602:Gtf2h2 UTSW 13 100,605,533 (GRCm39) missense probably benign 0.03
R0621:Gtf2h2 UTSW 13 100,625,433 (GRCm39) missense probably damaging 1.00
R0665:Gtf2h2 UTSW 13 100,617,562 (GRCm39) missense probably damaging 1.00
R4709:Gtf2h2 UTSW 13 100,605,523 (GRCm39) nonsense probably null
R4810:Gtf2h2 UTSW 13 100,617,510 (GRCm39) critical splice donor site probably null
R5262:Gtf2h2 UTSW 13 100,618,356 (GRCm39) unclassified probably benign
R5548:Gtf2h2 UTSW 13 100,617,544 (GRCm39) missense possibly damaging 0.92
R5741:Gtf2h2 UTSW 13 100,617,066 (GRCm39) missense probably benign 0.00
R6802:Gtf2h2 UTSW 13 100,617,051 (GRCm39) missense probably benign 0.39
R8355:Gtf2h2 UTSW 13 100,605,503 (GRCm39) missense possibly damaging 0.89
R9139:Gtf2h2 UTSW 13 100,617,778 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GGTAAACTTTCTTCATGTTTGAACTT -3'
(R):5'- CGACCTCAAAGGCAGGAAAG -3'

Sequencing Primer
(F):5'- GCTCAGTAGTTAACAACACTGGCTG -3'
(R):5'- TCAAAGGCAGGAAAGAGCTTTTATAC -3'
Posted On 2019-06-26