Incidental Mutation 'R6435:Runx1'
ID 518760
Institutional Source Beutler Lab
Gene Symbol Runx1
Ensembl Gene ENSMUSG00000022952
Gene Name runt related transcription factor 1
Synonyms AML1, Pebp2a2, runt domain, alpha subunit 2, Cbfa2
MMRRC Submission 044573-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6435 (G1)
Quality Score 133.008
Status Validated
Chromosome 16
Chromosomal Location 92398354-92622962 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 92441183 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 209 (S209T)
Ref Sequence ENSEMBL: ENSMUSP00000023673 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023673] [ENSMUST00000113956] [ENSMUST00000168195]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000023673
AA Change: S209T

PolyPhen 2 Score 0.532 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000023673
Gene: ENSMUSG00000022952
AA Change: S209T

DomainStartEndE-ValueType
low complexity region 42 55 N/A INTRINSIC
Pfam:Runt 65 194 4.5e-75 PFAM
low complexity region 205 220 N/A INTRINSIC
PDB:1B8X|A 333 374 2e-7 PDB
Pfam:RunxI 375 465 1.5e-42 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000113956
SMART Domains Protein: ENSMUSP00000109589
Gene: ENSMUSG00000022952

DomainStartEndE-ValueType
low complexity region 28 41 N/A INTRINSIC
Pfam:Runt 48 182 3.1e-81 PFAM
low complexity region 270 283 N/A INTRINSIC
Pfam:RunxI 294 387 4.9e-43 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000168195
AA Change: S195T

PolyPhen 2 Score 0.285 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000131079
Gene: ENSMUSG00000022952
AA Change: S195T

DomainStartEndE-ValueType
low complexity region 28 41 N/A INTRINSIC
Pfam:Runt 48 182 4.7e-82 PFAM
low complexity region 191 206 N/A INTRINSIC
low complexity region 334 347 N/A INTRINSIC
Pfam:RunxI 358 451 6.4e-43 PFAM
Meta Mutation Damage Score 0.1745 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.1%
  • 20x: 94.2%
Validation Efficiency 100% (32/32)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Core binding factor (CBF) is a heterodimeric transcription factor that binds to the core element of many enhancers and promoters. The protein encoded by this gene represents the alpha subunit of CBF and is thought to be involved in the development of normal hematopoiesis. Chromosomal translocations involving this gene are well-documented and have been associated with several types of leukemia. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mutations affect hematopoiesis, and in some cases result in defective angiogenesis and intraventricular hemorrhage. Null homozygotes die by embryonic day 12.5; heterozygotes have reduced erythroid and myeloid progenitor numbers. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 33 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abl1 A T 2: 31,691,561 (GRCm39) T1027S possibly damaging Het
Ablim1 T C 19: 57,049,787 (GRCm39) I159V possibly damaging Het
Adcy1 A G 11: 7,111,367 (GRCm39) N886S possibly damaging Het
Baz1b G A 5: 135,266,799 (GRCm39) D1203N probably damaging Het
Chmp2a A T 7: 12,766,701 (GRCm39) Y72* probably null Het
Col6a1 A T 10: 76,546,957 (GRCm39) I755N unknown Het
Defa24 T A 8: 22,224,690 (GRCm39) F46L possibly damaging Het
Eml2 G A 7: 18,935,088 (GRCm39) V432I probably damaging Het
Gcn1 A T 5: 115,749,081 (GRCm39) probably null Het
Gfpt2 A G 11: 49,726,478 (GRCm39) S628G probably benign Het
Hsdl2 C A 4: 59,610,668 (GRCm39) Q222K unknown Het
Ighv1-9 T A 12: 114,547,206 (GRCm39) I111F probably benign Het
Itch G A 2: 155,051,049 (GRCm39) D579N probably benign Het
Jdp2 A T 12: 85,655,132 (GRCm39) K65M probably damaging Het
Kif15 A T 9: 122,815,556 (GRCm39) E222V probably damaging Het
Map1b A G 13: 99,652,871 (GRCm39) V42A probably damaging Het
Mecom T A 3: 30,034,398 (GRCm39) E426V probably damaging Het
Meiosin T C 7: 18,834,844 (GRCm39) probably benign Het
Mfsd6 G T 1: 52,748,603 (GRCm39) Y87* probably null Het
Mybpc2 A G 7: 44,155,481 (GRCm39) V924A possibly damaging Het
Naip6 A T 13: 100,431,249 (GRCm39) M1196K probably benign Het
Nscme3l T C 19: 5,553,446 (GRCm39) I112V probably benign Het
Or52n5 A G 7: 104,588,041 (GRCm39) M103V probably damaging Het
Pcdh9 G A 14: 94,125,280 (GRCm39) P297S probably benign Het
Pold1 G A 7: 44,188,202 (GRCm39) R559C probably damaging Het
Rgs21 A G 1: 144,395,565 (GRCm39) F108L probably damaging Het
Sdccag8 G T 1: 176,642,428 (GRCm39) probably benign Het
Smc1b C T 15: 84,976,232 (GRCm39) R825Q probably benign Het
Srgap1 T C 10: 121,636,732 (GRCm39) D741G possibly damaging Het
Srsf11 C T 3: 157,728,981 (GRCm39) probably benign Homo
Tsc1 G A 2: 28,566,464 (GRCm39) V627M probably benign Het
Vmn2r106 C T 17: 20,488,725 (GRCm39) C558Y probably damaging Het
Zfp612 A G 8: 110,815,952 (GRCm39) I347M probably damaging Het
Other mutations in Runx1
AlleleSourceChrCoordTypePredicted EffectPPH Score
Funyon UTSW 16 92,402,544 (GRCm39) makesense probably null
G1Funyon:Runx1 UTSW 16 92,402,544 (GRCm39) makesense probably null
PIT4382001:Runx1 UTSW 16 92,410,648 (GRCm39) missense probably damaging 0.97
R0055:Runx1 UTSW 16 92,441,029 (GRCm39) splice site probably benign
R0315:Runx1 UTSW 16 92,402,655 (GRCm39) missense probably damaging 0.99
R1353:Runx1 UTSW 16 92,485,939 (GRCm39) nonsense probably null
R4059:Runx1 UTSW 16 92,441,134 (GRCm39) missense probably benign 0.09
R4771:Runx1 UTSW 16 92,492,629 (GRCm39) missense possibly damaging 0.70
R4977:Runx1 UTSW 16 92,441,235 (GRCm39) critical splice acceptor site probably null
R5631:Runx1 UTSW 16 92,492,451 (GRCm39) missense possibly damaging 0.94
R6257:Runx1 UTSW 16 92,492,799 (GRCm39) unclassified probably benign
R8301:Runx1 UTSW 16 92,402,544 (GRCm39) makesense probably null
R9239:Runx1 UTSW 16 92,402,935 (GRCm39) missense probably damaging 1.00
R9298:Runx1 UTSW 16 92,441,147 (GRCm39) missense possibly damaging 0.71
R9389:Runx1 UTSW 16 92,410,568 (GRCm39) missense possibly damaging 0.95
R9404:Runx1 UTSW 16 92,485,915 (GRCm39) missense probably benign 0.04
Z1088:Runx1 UTSW 16 92,402,680 (GRCm39) missense probably damaging 1.00
Z1176:Runx1 UTSW 16 92,485,989 (GRCm39) missense possibly damaging 0.83
Predicted Primers PCR Primer
(F):5'- CTTAGAGCACCCAGAAAGGC -3'
(R):5'- GGCAATGTCCAACAAGCTC -3'

Sequencing Primer
(F):5'- AGCCCCGGTGCTTTCTG -3'
(R):5'- CAAGCTCACCTTGGGGG -3'
Posted On 2018-05-24