Incidental Mutation 'R5994:Hoxa2'
ID 480996
Institutional Source Beutler Lab
Gene Symbol Hoxa2
Ensembl Gene ENSMUSG00000014704
Gene Name homeobox A2
Synonyms Hox-1.11
MMRRC Submission 044173-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5994 (G1)
Quality Score 110.008
Status Not validated
Chromosome 6
Chromosomal Location 52139397-52141811 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to G at 52141372 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Arginine at position 85 (S85R)
Ref Sequence ENSEMBL: ENSMUSP00000014848 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000014848] [ENSMUST00000114434] [ENSMUST00000128102]
AlphaFold P31245
Predicted Effect possibly damaging
Transcript: ENSMUST00000014848
AA Change: S85R

PolyPhen 2 Score 0.734 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000014848
Gene: ENSMUSG00000014704
AA Change: S85R

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 benign
Transcript: ENSMUST00000128102
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132559
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155922
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184649
Predicted Effect noncoding transcript
Transcript: ENSMUST00000183920
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184680
Predicted Effect noncoding transcript
Transcript: ENSMUST00000159006
Predicted Effect noncoding transcript
Transcript: ENSMUST00000189230
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.4%
  • 20x: 91.7%
Validation Efficiency
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: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A2m A T 6: 121,647,862 (GRCm39) H1118L probably benign Het
Abca8b A G 11: 109,840,592 (GRCm39) probably null Het
Abcb5 A T 12: 118,928,995 (GRCm39) probably null Het
Adcy6 A T 15: 98,491,545 (GRCm39) I1016N probably damaging Het
Afg3l2 A T 18: 67,562,140 (GRCm39) C312S probably damaging Het
Ano8 C T 8: 71,937,478 (GRCm39) V89M probably damaging Het
Arhgap21 C T 2: 20,886,187 (GRCm39) G330D possibly damaging Het
Caskin1 T C 17: 24,715,935 (GRCm39) L195P probably damaging Het
Cfap54 A G 10: 92,874,943 (GRCm39) I514T probably damaging Het
Ctdsp2 G A 10: 126,831,689 (GRCm39) probably benign Het
Cyp4x1 T C 4: 114,979,142 (GRCm39) I152V probably benign Het
Dglucy G A 12: 100,808,959 (GRCm39) R219Q probably benign Het
Disp3 G T 4: 148,338,741 (GRCm39) A810E possibly damaging Het
Dtx4 T C 19: 12,478,517 (GRCm39) Y22C probably damaging Het
Edaradd A T 13: 12,493,377 (GRCm39) I105N probably damaging Het
Eepd1 C T 9: 25,514,749 (GRCm39) P519S probably damaging Het
Fscn3 A T 6: 28,430,294 (GRCm39) S155C probably benign Het
Gm10134 A T 2: 28,396,258 (GRCm39) E51V probably damaging Het
Gm7247 C T 14: 51,601,805 (GRCm39) S26F probably benign Het
Golga7 T C 8: 23,740,281 (GRCm39) E83G probably benign Het
Gpr12 T C 5: 146,520,241 (GRCm39) H227R probably damaging Het
Hrnr T C 3: 93,239,607 (GRCm39) S3282P unknown Het
Ift74 C A 4: 94,579,961 (GRCm39) T543K possibly damaging Het
Klf10 C A 15: 38,296,285 (GRCm39) R420L probably damaging Het
Krt77 T A 15: 101,771,290 (GRCm39) I338F probably damaging Het
Limch1 A T 5: 67,131,965 (GRCm39) S152C probably damaging Het
Mgat4e T A 1: 134,469,234 (GRCm39) H270L probably benign Het
Myrf A T 19: 10,196,481 (GRCm39) L504Q probably null Het
Nckipsd A G 9: 108,691,176 (GRCm39) Q366R probably benign Het
Npy5r A T 8: 67,134,751 (GRCm39) V14D probably benign Het
Nrap T A 19: 56,340,031 (GRCm39) R830* probably null Het
Ogfrl1 A T 1: 23,418,070 (GRCm39) Y103N probably damaging Het
Or10g7 A T 9: 39,905,519 (GRCm39) R138* probably null Het
P2rx4 T A 5: 122,863,142 (GRCm39) L232H probably damaging Het
Pabpc2 A T 18: 39,906,947 (GRCm39) T71S probably benign Het
Paip2b C A 6: 83,785,867 (GRCm39) S121I probably damaging Het
Pofut1 C T 2: 153,103,149 (GRCm39) T261I possibly damaging Het
Ppp6c G T 2: 39,101,004 (GRCm39) T46K possibly damaging Het
Prkd2 C A 7: 16,584,261 (GRCm39) H371Q probably benign Het
Prrc2c A T 1: 162,501,725 (GRCm39) probably null Het
Psd3 C T 8: 68,172,620 (GRCm39) A894T probably damaging Het
Pygm A T 19: 6,448,073 (GRCm39) probably null Het
Pzp A T 6: 128,468,560 (GRCm39) M989K probably damaging Het
Ralgapa2 A T 2: 146,203,373 (GRCm39) S1159T probably benign Het
Rapgefl1 T C 11: 98,740,986 (GRCm39) F575L probably benign Het
Rassf6 A G 5: 90,765,627 (GRCm39) L28S probably damaging Het
Rbp3 G T 14: 33,676,857 (GRCm39) K268N probably damaging Het
Rela C T 19: 5,697,092 (GRCm39) T433M possibly damaging Het
Rnf103 T A 6: 71,473,894 (GRCm39) S102R probably damaging Het
Scarf2 A G 16: 17,624,243 (GRCm39) N516S probably damaging Het
Sdcbp2 T C 2: 151,429,403 (GRCm39) I241T probably damaging Het
Septin7 T C 9: 25,199,494 (GRCm39) I131T possibly damaging Het
Sh3pxd2b T C 11: 32,357,570 (GRCm39) F191L probably damaging Het
Siglec15 C A 18: 78,090,590 (GRCm39) C236F probably damaging Het
Slc11a2 T C 15: 100,295,562 (GRCm39) T520A probably benign Het
Slc26a11 C A 11: 119,270,738 (GRCm39) F553L probably benign Het
Smchd1 G A 17: 71,672,404 (GRCm39) P1596S possibly damaging Het
Taar7b A G 10: 23,876,246 (GRCm39) H137R probably damaging Het
Thap12 T A 7: 98,365,237 (GRCm39) C468* probably null Het
Timp4 C T 6: 115,224,315 (GRCm39) G118D probably damaging Het
Tnnt3 A G 7: 142,065,003 (GRCm39) K48E probably damaging Het
Trmt10a T A 3: 137,862,475 (GRCm39) I255N probably damaging Het
Ttll10 T C 4: 156,133,189 (GRCm39) probably null Het
Tut7 T G 13: 59,937,023 (GRCm39) Y806S probably damaging Het
Ube4b A G 4: 149,457,389 (GRCm39) Y283H probably damaging Het
Ucp1 G T 8: 84,020,567 (GRCm39) V126L possibly damaging Het
Unc13b T A 4: 43,172,596 (GRCm39) probably benign Het
Vps13b T C 15: 35,875,918 (GRCm39) S2768P probably damaging Het
Zfp101 T A 17: 33,599,936 (GRCm39) M607L probably benign Het
Zfp292 C T 4: 34,805,464 (GRCm39) V2527M possibly damaging Het
Zfp503 T A 14: 22,035,630 (GRCm39) T429S possibly damaging Het
Other mutations in Hoxa2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00331:Hoxa2 APN 6 52,140,497 (GRCm39) missense probably damaging 1.00
R0111:Hoxa2 UTSW 6 52,141,467 (GRCm39) splice site probably null
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
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'- TTCCCTCGAAGCTCATGGTC -3'
(R):5'- CCTGTCGCTGATACATTTCAAAGTTC -3'

Sequencing Primer
(F):5'- AACCGCTCCTAGGGAAGC -3'
(R):5'- GTTCATCAATCAAGACCTCGACG -3'
Posted On 2017-06-26