Incidental Mutation 'R0111:Hoxa2'
ID 20449
Institutional Source Beutler Lab
Gene Symbol Hoxa2
Ensembl Gene ENSMUSG00000014704
Gene Name homeobox A2
Synonyms Hox-1.11
MMRRC Submission 038397-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0111 (G1)
Quality Score 225
Status Validated (trace)
Chromosome 6
Chromosomal Location 52139397-52141811 bp(-) (GRCm39)
Type of Mutation splice site
DNA Base Change (assembly) T to G at 52141467 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000140776 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000014848] [ENSMUST00000114434] [ENSMUST00000128102]
AlphaFold P31245
Predicted Effect probably damaging
Transcript: ENSMUST00000014848
AA Change: E53A

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000014848
Gene: ENSMUSG00000014704
AA Change: E53A

DomainStartEndE-ValueType
low complexity region 34 48 N/A INTRINSIC
low complexity region 101 116 N/A INTRINSIC
HOX 139 201 2.37e-28 SMART
low complexity region 214 227 N/A INTRINSIC
low complexity region 332 367 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000114434
SMART Domains Protein: ENSMUSP00000110077
Gene: ENSMUSG00000079560

DomainStartEndE-ValueType
low complexity region 76 131 N/A INTRINSIC
HOX 192 254 3.35e-28 SMART
low complexity region 287 302 N/A INTRINSIC
low complexity region 304 326 N/A INTRINSIC
Pfam:DUF4074 377 441 9e-32 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000114435
Predicted Effect probably null
Transcript: ENSMUST00000128102
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132559
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155922
Predicted Effect noncoding transcript
Transcript: ENSMUST00000159006
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184680
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184649
Predicted Effect noncoding transcript
Transcript: ENSMUST00000183920
Predicted Effect noncoding transcript
Transcript: ENSMUST00000189230
Meta Mutation Damage Score 0.1913 question?
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.2%
  • 10x: 96.2%
  • 20x: 92.8%
Validation Efficiency 100% (65/65)
MGI Phenotype FUNCTION: This gene is located in a cluster of developmentally and temporally regulated genes on chromosome 6 encoding proteins involved in pattern formation. These proteins contain a characteristic DNA-binding motif called a homeodomain and function in transcriptional regulation. There are four distinct clusters of related genes on chromosomes 2, 6, 11, and 15. The protein encoded by this gene is expressed in rhombomere 2 and is important for hindbrain formation in the early embryo. [provided by RefSeq, Mar 2013]
PHENOTYPE: Mutant homozygotes lack skeletal elements normally derived from the second branchial arch and show duplication of elements derived from the first branchial arch, such as ossification centers of the middle ear. Mutants die perinatally with cleft palate. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 59 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgre4 A T 17: 56,124,073 (GRCm39) H491L possibly damaging Het
Adgrg3 T C 8: 95,761,738 (GRCm39) probably benign Het
Arhgap5 T C 12: 52,606,743 (GRCm39) probably benign Het
Asic1 T C 15: 99,594,864 (GRCm39) Y334H probably damaging Het
Calcr T A 6: 3,717,157 (GRCm39) D101V probably damaging Het
Cdh2 A T 18: 16,907,566 (GRCm39) N57K probably benign Het
Clec4d C A 6: 123,245,006 (GRCm39) Y95* probably null Het
Cracr2a A G 6: 127,581,024 (GRCm39) T67A probably benign Het
Dennd5a A T 7: 109,533,961 (GRCm39) V53D probably damaging Het
Dnah7a T C 1: 53,507,843 (GRCm39) D3076G probably benign Het
Espnl T C 1: 91,272,464 (GRCm39) M608T probably benign Het
Fam149a C T 8: 45,794,183 (GRCm39) probably benign Het
Flnc T C 6: 29,454,339 (GRCm39) V1884A probably damaging Het
Helz2 A C 2: 180,879,595 (GRCm39) S674R probably benign Het
Ifi47 T A 11: 48,986,897 (GRCm39) N221K probably damaging Het
Ipo9 A G 1: 135,333,662 (GRCm39) V340A probably damaging Het
Kalrn A T 16: 33,851,960 (GRCm39) N373K probably damaging Het
Kif26a T C 12: 112,129,771 (GRCm39) probably benign Het
Kiss1r A G 10: 79,754,523 (GRCm39) T6A possibly damaging Het
Lama1 A T 17: 68,044,493 (GRCm39) I131F probably damaging Het
Nefm T C 14: 68,361,991 (GRCm39) D91G probably benign Het
Nos3 C T 5: 24,577,702 (GRCm39) T572I probably damaging Het
Notch2 T C 3: 98,046,077 (GRCm39) F1710L probably benign Het
Or13e8 T C 4: 43,696,648 (GRCm39) N175S probably damaging Het
Or6c6c T A 10: 129,541,146 (GRCm39) I133N probably damaging Het
Ostm1 T C 10: 42,555,254 (GRCm39) L92P probably damaging Het
Pcdh15 T A 10: 74,462,651 (GRCm39) Y1445* probably null Het
Pde1b T C 15: 103,411,940 (GRCm39) S14P probably benign Het
Pitpna T C 11: 75,516,310 (GRCm39) V265A probably benign Het
Plec G T 15: 76,062,846 (GRCm39) T2476K probably damaging Het
Pold2 A G 11: 5,826,760 (GRCm39) L58P probably damaging Het
Ppp3cc C T 14: 70,493,808 (GRCm39) probably null Het
Prss36 A G 7: 127,533,717 (GRCm39) L530P probably damaging Het
Ptpn13 T C 5: 103,728,629 (GRCm39) probably benign Het
Ptpn23 T C 9: 110,214,691 (GRCm39) D1570G probably damaging Het
Rab42 T C 4: 132,029,676 (GRCm39) D182G possibly damaging Het
Rbm27 T A 18: 42,438,737 (GRCm39) probably benign Het
Rp1 T C 1: 4,414,983 (GRCm39) E2043G probably damaging Het
Rufy3 C T 5: 88,778,443 (GRCm39) S341F probably damaging Het
Samd9l C T 6: 3,374,946 (GRCm39) V772I possibly damaging Het
Scaper A G 9: 55,510,074 (GRCm39) M654T probably benign Het
Shld2 T C 14: 33,989,686 (GRCm39) K407E probably damaging Het
Sipa1l3 G A 7: 29,047,743 (GRCm39) P333S probably damaging Het
Slc30a10 C A 1: 185,187,744 (GRCm39) R162S probably benign Het
Spryd3 A T 15: 102,036,972 (GRCm39) probably null Het
Tas2r110 T C 6: 132,845,166 (GRCm39) F66L probably benign Het
Tent5c T C 3: 100,380,102 (GRCm39) D218G probably damaging Het
Thap2 T C 10: 115,208,532 (GRCm39) N196S probably benign Het
Themis2 C A 4: 132,517,236 (GRCm39) R88L probably benign Het
Trip12 A T 1: 84,736,854 (GRCm39) probably benign Het
Ube3b T A 5: 114,528,437 (GRCm39) probably benign Het
Usp20 T A 2: 30,892,624 (GRCm39) H64Q probably damaging Het
Vmn2r100 C A 17: 19,742,382 (GRCm39) P252Q possibly damaging Het
Vmn2r15 T C 5: 109,435,022 (GRCm39) R561G possibly damaging Het
Vsig10l A G 7: 43,117,525 (GRCm39) D604G probably damaging Het
Wdr90 A G 17: 26,067,418 (GRCm39) probably benign Het
Xirp2 A T 2: 67,338,722 (GRCm39) N321I probably damaging Het
Zfp595 A G 13: 67,468,984 (GRCm39) F11S possibly damaging Het
Zfp953 T A 13: 67,491,139 (GRCm39) H271L probably damaging Het
Other mutations in Hoxa2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00331:Hoxa2 APN 6 52,140,497 (GRCm39) missense probably damaging 1.00
R0612:Hoxa2 UTSW 6 52,140,540 (GRCm39) missense probably damaging 1.00
R1479:Hoxa2 UTSW 6 52,140,320 (GRCm39) missense probably damaging 0.97
R1992:Hoxa2 UTSW 6 52,141,576 (GRCm39) missense probably damaging 0.97
R2315:Hoxa2 UTSW 6 52,139,871 (GRCm39) unclassified probably benign
R5703:Hoxa2 UTSW 6 52,140,243 (GRCm39) missense probably damaging 0.98
R5994:Hoxa2 UTSW 6 52,141,372 (GRCm39) missense possibly damaging 0.73
R6168:Hoxa2 UTSW 6 52,140,461 (GRCm39) missense probably damaging 1.00
R7483:Hoxa2 UTSW 6 52,141,279 (GRCm39) missense probably benign 0.01
R7573:Hoxa2 UTSW 6 52,140,283 (GRCm39) missense probably benign 0.25
R7708:Hoxa2 UTSW 6 52,141,542 (GRCm39) missense probably damaging 0.99
R8215:Hoxa2 UTSW 6 52,140,041 (GRCm39) missense probably damaging 1.00
R8548:Hoxa2 UTSW 6 52,140,098 (GRCm39) missense probably damaging 1.00
R8683:Hoxa2 UTSW 6 52,141,540 (GRCm39) missense possibly damaging 0.46
R8936:Hoxa2 UTSW 6 52,140,517 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TCCTTCATCCAGGGATACTCAGGC -3'
(R):5'- ACACCCCAGCAGCGATCTTCTATG -3'

Sequencing Primer
(F):5'- ATACTCAGGCGGCTGCAGGGCGCC -3'
(R):5'- TTTTCCTCCGAGGGGGC -3'
Posted On 2013-04-11