Incidental Mutation 'R0815:Supt4a'
ID 99135
Institutional Source Beutler Lab
Gene Symbol Supt4a
Ensembl Gene ENSMUSG00000020485
Gene Name SPT4A, DSIF elongation factor subunit
Synonyms Supt4h1, Supt4h
MMRRC Submission 038995-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0815 (G1)
Quality Score 222
Status Validated
Chromosome 11
Chromosomal Location 87628378-87634449 bp(+) (GRCm39)
Type of Mutation unclassified
DNA Base Change (assembly) T to A at 87628409 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000130685 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000040089] [ENSMUST00000092800] [ENSMUST00000093955] [ENSMUST00000121782] [ENSMUST00000141169] [ENSMUST00000152700] [ENSMUST00000165679]
AlphaFold P63271
Predicted Effect probably benign
Transcript: ENSMUST00000040089
SMART Domains Protein: ENSMUSP00000044241
Gene: ENSMUSG00000034177

DomainStartEndE-ValueType
PDB:4KNG|F 1 71 7e-32 PDB
transmembrane domain 72 91 N/A INTRINSIC
RING 145 185 6.43e-8 SMART
low complexity region 337 351 N/A INTRINSIC
low complexity region 366 376 N/A INTRINSIC
low complexity region 420 431 N/A INTRINSIC
low complexity region 491 516 N/A INTRINSIC
low complexity region 646 654 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000092800
SMART Domains Protein: ENSMUSP00000090476
Gene: ENSMUSG00000034177

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
PDB:4KNG|F 44 198 6e-93 PDB
transmembrane domain 199 218 N/A INTRINSIC
RING 272 312 6.43e-8 SMART
low complexity region 464 478 N/A INTRINSIC
low complexity region 493 503 N/A INTRINSIC
low complexity region 547 558 N/A INTRINSIC
low complexity region 618 643 N/A INTRINSIC
low complexity region 773 781 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000093955
SMART Domains Protein: ENSMUSP00000091487
Gene: ENSMUSG00000020485

DomainStartEndE-ValueType
Spt4 13 90 3.22e-43 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000121782
SMART Domains Protein: ENSMUSP00000112748
Gene: ENSMUSG00000034177

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
PDB:4KNG|F 44 157 6e-54 PDB
transmembrane domain 158 177 N/A INTRINSIC
RING 231 271 6.43e-8 SMART
low complexity region 423 437 N/A INTRINSIC
low complexity region 452 462 N/A INTRINSIC
low complexity region 506 517 N/A INTRINSIC
low complexity region 577 602 N/A INTRINSIC
low complexity region 732 740 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000141169
SMART Domains Protein: ENSMUSP00000117762
Gene: ENSMUSG00000020485

DomainStartEndE-ValueType
Pfam:Spt4 13 76 3.3e-20 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000150866
Predicted Effect probably benign
Transcript: ENSMUST00000152700
SMART Domains Protein: ENSMUSP00000118619
Gene: ENSMUSG00000020485

DomainStartEndE-ValueType
Spt4 13 73 7.28e-10 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000165679
SMART Domains Protein: ENSMUSP00000130685
Gene: ENSMUSG00000034177

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
PDB:4KNG|F 44 198 6e-93 PDB
transmembrane domain 199 218 N/A INTRINSIC
RING 272 312 6.43e-8 SMART
low complexity region 464 478 N/A INTRINSIC
low complexity region 493 503 N/A INTRINSIC
low complexity region 547 558 N/A INTRINSIC
low complexity region 618 643 N/A INTRINSIC
low complexity region 773 781 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 96.5%
  • 20x: 91.3%
Validation Efficiency 97% (58/60)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the small subunit of DRB (5,6-dichloro-1-beta-d-ribofuranosylbenzimidazole) sensitivity-inducing factor (DSIF) complex, which regulates mRNA processing and transcription elongation by RNA polymerase II. The encoded protein is localized to the nucleus and interacts with the large subunit (SUPT5H) to form the DSIF complex. Related pseudogenes have been identified on chromosomes 2 and 12. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Nov 2012]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality at E7.5. Mice heterozygous for a knock-out allele partially suppress the motor defects and premature death associated with Tg(HDexon1)62Gpb. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb5 A G 12: 118,865,184 (GRCm39) probably benign Het
Abcf2 A T 5: 24,772,268 (GRCm39) Y487N probably damaging Het
Adcy4 T C 14: 56,021,056 (GRCm39) Y27C probably damaging Het
Atp2a2 T C 5: 122,609,299 (GRCm39) I188V probably benign Het
Cacna1s A T 1: 136,040,695 (GRCm39) I1231F possibly damaging Het
Capn7 T A 14: 31,091,714 (GRCm39) C704S possibly damaging Het
Celsr2 G T 3: 108,308,617 (GRCm39) T1770K possibly damaging Het
Chmp7 C T 14: 69,956,899 (GRCm39) M336I probably benign Het
Cul9 T C 17: 46,848,748 (GRCm39) probably null Het
Dpp10 A G 1: 123,360,658 (GRCm39) probably null Het
Dscaml1 A G 9: 45,656,372 (GRCm39) I1571V probably benign Het
Eif3j2 T A 18: 43,610,036 (GRCm39) Y259F probably benign Het
Erc2 A C 14: 27,747,105 (GRCm39) N345T probably benign Het
Fbxo21 T C 5: 118,133,573 (GRCm39) probably benign Het
Frmd8 A T 19: 5,915,084 (GRCm39) probably benign Het
Gfm1 T C 3: 67,381,928 (GRCm39) S705P probably damaging Het
Gucy1b2 T C 14: 62,656,511 (GRCm39) D282G probably benign Het
H2-Ab1 T C 17: 34,486,328 (GRCm39) I129T probably damaging Het
H2-M10.3 T A 17: 36,677,582 (GRCm39) Y232F probably damaging Het
Lipm A T 19: 34,096,161 (GRCm39) T326S probably benign Het
Lrrc8c T C 5: 105,756,400 (GRCm39) L725P probably damaging Het
Map3k19 A G 1: 127,762,375 (GRCm39) probably benign Het
Med31 T A 11: 72,104,657 (GRCm39) N50I probably damaging Het
Myo15b T G 11: 115,757,162 (GRCm39) probably benign Het
Nemp1 T C 10: 127,528,893 (GRCm39) L199S probably damaging Het
Nod2 G A 8: 89,399,290 (GRCm39) probably benign Het
Oga C T 19: 45,771,425 (GRCm39) A49T probably benign Het
Or2ak6 A G 11: 58,593,435 (GRCm39) R303G possibly damaging Het
Or5b21 A G 19: 12,840,008 (GRCm39) I290V probably benign Het
Parva G A 7: 112,167,071 (GRCm39) V215M probably damaging Het
Phf1 T C 17: 27,156,114 (GRCm39) probably benign Het
Plscr1l1 A T 9: 92,233,140 (GRCm39) I88L possibly damaging Het
Ppp1r12c G T 7: 4,489,365 (GRCm39) Q240K probably damaging Het
Ralgapa1 A T 12: 55,809,466 (GRCm39) Y436* probably null Het
Ralgapa1 C A 12: 55,829,562 (GRCm39) probably benign Het
Rbm11 C T 16: 75,393,525 (GRCm39) R74C probably damaging Het
Robo3 A G 9: 37,333,479 (GRCm39) V744A probably damaging Het
Rsbn1 T G 3: 103,861,469 (GRCm39) S522A probably damaging Het
Scel T A 14: 103,823,916 (GRCm39) S381R possibly damaging Het
Sec31b G A 19: 44,506,612 (GRCm39) Q909* probably null Het
Slc38a11 T A 2: 65,184,124 (GRCm39) I176L possibly damaging Het
Slc39a4 C T 15: 76,496,839 (GRCm39) D574N probably damaging Het
Slc44a1 T G 4: 53,536,421 (GRCm39) V199G possibly damaging Het
Sltm A G 9: 70,469,190 (GRCm39) T150A probably benign Het
Son C A 16: 91,452,372 (GRCm39) A373D probably damaging Het
Sp140 C T 1: 85,547,772 (GRCm39) probably benign Het
Speg A G 1: 75,392,036 (GRCm39) Y1606C probably damaging Het
Srgap1 A T 10: 121,621,379 (GRCm39) V1061D probably damaging Het
Stat5a A G 11: 100,765,908 (GRCm39) probably null Het
Teddm1b A G 1: 153,750,638 (GRCm39) K149R possibly damaging Het
Thnsl2 A T 6: 71,111,208 (GRCm39) L220* probably null Het
Tinf2 G A 14: 55,917,566 (GRCm39) P308S probably benign Het
Tmem131l A G 3: 83,847,879 (GRCm39) S329P probably benign Het
Tnf T C 17: 35,420,120 (GRCm39) probably benign Het
Upp2 A G 2: 58,661,568 (GRCm39) T144A probably benign Het
Vmn2r94 T G 17: 18,477,973 (GRCm39) Q146P probably damaging Het
Zfhx4 T A 3: 5,310,375 (GRCm39) S919R possibly damaging Het
Other mutations in Supt4a
AlleleSourceChrCoordTypePredicted EffectPPH Score
R0595:Supt4a UTSW 11 87,633,982 (GRCm39) splice site probably null
R0864:Supt4a UTSW 11 87,633,913 (GRCm39) missense probably benign 0.15
R5566:Supt4a UTSW 11 87,634,113 (GRCm39) missense probably benign 0.01
R7034:Supt4a UTSW 11 87,634,084 (GRCm39) missense probably damaging 0.99
R7036:Supt4a UTSW 11 87,634,084 (GRCm39) missense probably damaging 0.99
R8970:Supt4a UTSW 11 87,633,645 (GRCm39) missense probably benign 0.00
R9135:Supt4a UTSW 11 87,633,624 (GRCm39) missense probably benign 0.12
Predicted Primers
Posted On 2014-01-10