Incidental Mutation 'R0315:Runx1'
ID 65255
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 038525-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0315 (G1)
Quality Score 100
Status Validated
Chromosome 16
Chromosomal Location 92398354-92622962 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 92402655 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Serine at position 429 (N429S)
Ref Sequence ENSEMBL: ENSMUSP00000023673 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023673] [ENSMUST00000113956] [ENSMUST00000168195]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000023673
AA Change: N429S

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000023673
Gene: ENSMUSG00000022952
AA Change: N429S

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 possibly damaging
Transcript: ENSMUST00000113956
AA Change: N351S

PolyPhen 2 Score 0.696 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000109589
Gene: ENSMUSG00000022952
AA Change: N351S

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 possibly damaging
Transcript: ENSMUST00000168195
AA Change: N415S

PolyPhen 2 Score 0.825 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000131079
Gene: ENSMUSG00000022952
AA Change: N415S

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 0.1652 question?
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 97.8%
  • 10x: 94.9%
  • 20x: 88.9%
Validation Efficiency 100% (42/42)
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: 42 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aars2 G A 17: 45,826,378 (GRCm39) R409Q possibly damaging Het
Ank3 A T 10: 69,838,347 (GRCm39) Q825L probably damaging Het
Ap1g1 A G 8: 110,545,667 (GRCm39) I107V probably benign Het
Bub1b A T 2: 118,457,457 (GRCm39) probably benign Het
Cd86 C T 16: 36,441,306 (GRCm39) V54I possibly damaging Het
Dpys T G 15: 39,720,734 (GRCm39) I9L probably benign Het
Fbxl17 G A 17: 63,663,846 (GRCm39) R67C probably damaging Het
Flg2 G T 3: 93,122,029 (GRCm39) G1400C unknown Het
Gm28042 T C 2: 119,869,538 (GRCm39) L634P probably damaging Het
Gm6712 G A 17: 17,536,380 (GRCm39) noncoding transcript Het
Gpbp1 T G 13: 111,573,072 (GRCm39) E360A possibly damaging Het
Hmgn1 A C 16: 95,926,017 (GRCm39) I52R probably benign Het
Ing2 A C 8: 48,122,125 (GRCm39) M141R probably benign Het
Klhl2 A T 8: 65,196,053 (GRCm39) Y563* probably null Het
Lrrc9 A G 12: 72,502,802 (GRCm39) T258A probably damaging Het
Map1b A T 13: 99,567,624 (GRCm39) I1699N unknown Het
Map2k5 A T 9: 63,210,433 (GRCm39) H185Q probably damaging Het
Mpv17l A T 16: 13,758,863 (GRCm39) I96L probably benign Het
Mroh1 C T 15: 76,311,800 (GRCm39) A511V possibly damaging Het
Nop53 T C 7: 15,679,235 (GRCm39) D90G probably damaging Het
Or10k2 T C 8: 84,268,001 (GRCm39) V76A possibly damaging Het
Or5b97 A T 19: 12,878,598 (GRCm39) V182D possibly damaging Het
Or5w20 A T 2: 87,727,410 (GRCm39) Y289F probably damaging Het
Or6c209 T A 10: 129,483,366 (GRCm39) I123N probably damaging Het
Pkd2 T A 5: 104,607,716 (GRCm39) S72T possibly damaging Het
Prc1 T C 7: 79,963,284 (GRCm39) S587P probably damaging Het
Rdh7 G T 10: 127,724,265 (GRCm39) T73K possibly damaging Het
Skint7 G A 4: 111,845,315 (GRCm39) A376T possibly damaging Het
Slc16a14 T C 1: 84,890,217 (GRCm39) I363V possibly damaging Het
Smarcal1 C T 1: 72,634,970 (GRCm39) Q350* probably null Het
Soat1 T A 1: 156,268,083 (GRCm39) K275* probably null Het
Speg T C 1: 75,391,780 (GRCm39) V1571A possibly damaging Het
Stat5b G C 11: 100,679,286 (GRCm39) D605E probably benign Het
Susd4 G A 1: 182,686,077 (GRCm39) R209H probably benign Het
Tlr1 T G 5: 65,084,271 (GRCm39) D102A probably damaging Het
Tm4sf5 A G 11: 70,401,462 (GRCm39) N154D probably damaging Het
Tmigd3 T A 3: 105,824,085 (GRCm39) M18K probably damaging Het
Ube2h A T 6: 30,241,412 (GRCm39) V86E probably damaging Het
Utp20 A G 10: 88,643,283 (GRCm39) L613P probably damaging Het
Vmn2r117 G A 17: 23,679,139 (GRCm39) S695L probably benign Het
Washc5 T C 15: 59,213,825 (GRCm39) D427G probably damaging Het
Zfp462 T A 4: 55,079,314 (GRCm39) F2403I 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
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
R6435:Runx1 UTSW 16 92,441,183 (GRCm39) missense possibly damaging 0.53
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'- AGAAGCATTCACAGTTTCCCTCCG -3'
(R):5'- ACTCTTTGTGTCAGAGGCACTCTCC -3'

Sequencing Primer
(F):5'- TTCCTGGTGGCCTCCAAG -3'
(R):5'- CACTCTGGCAGTCTAGGAAG -3'
Posted On 2013-08-08