Incidental Mutation 'R6852:Ddx39a'
ID 535033
Institutional Source Beutler Lab
Gene Symbol Ddx39a
Ensembl Gene ENSMUSG00000005481
Gene Name DEAD box helicase 39a
Synonyms BAT1, 2610307C23Rik, Ddx39
MMRRC Submission 045023-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.930) question?
Stock # R6852 (G1)
Quality Score 225.009
Status Not validated
Chromosome 8
Chromosomal Location 84441806-84453521 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 84449646 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 417 (I417T)
Ref Sequence ENSEMBL: ENSMUSP00000148329 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000002964] [ENSMUST00000019576] [ENSMUST00000075843] [ENSMUST00000109802] [ENSMUST00000109810] [ENSMUST00000140521] [ENSMUST00000166939] [ENSMUST00000172396] [ENSMUST00000212949]
AlphaFold Q8VDW0
Predicted Effect probably benign
Transcript: ENSMUST00000002964
SMART Domains Protein: ENSMUSP00000002964
Gene: ENSMUSG00000002885

DomainStartEndE-ValueType
EGF 30 68 1.63e1 SMART
EGF_CA 69 119 5.92e-8 SMART
EGF_CA 120 167 1.78e-11 SMART
GPS 384 430 2.18e-8 SMART
Pfam:Dicty_CAR 431 703 1.3e-8 PFAM
Pfam:7tm_2 432 672 8.1e-68 PFAM
low complexity region 704 714 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000019576
AA Change: I417T

PolyPhen 2 Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000019576
Gene: ENSMUSG00000005481
AA Change: I417T

DomainStartEndE-ValueType
low complexity region 5 18 N/A INTRINSIC
DEXDc 63 264 4.06e-54 SMART
HELICc 300 381 9.09e-25 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000075843
SMART Domains Protein: ENSMUSP00000075240
Gene: ENSMUSG00000002885

DomainStartEndE-ValueType
EGF 30 68 1.63e1 SMART
EGF_CA 69 119 5.92e-8 SMART
EGF_CA 165 213 1.38e-8 SMART
EGF_CA 214 261 1.78e-11 SMART
GPS 478 524 2.18e-8 SMART
Pfam:Dicty_CAR 525 798 4.6e-8 PFAM
Pfam:7tm_2 526 766 5.3e-68 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000109802
SMART Domains Protein: ENSMUSP00000105427
Gene: ENSMUSG00000002885

DomainStartEndE-ValueType
EGF 30 68 1.63e1 SMART
EGF_CA 69 119 5.92e-8 SMART
EGF_CA 120 168 1.38e-8 SMART
EGF_CA 169 216 1.78e-11 SMART
GPS 433 479 2.18e-8 SMART
Pfam:Dicty_CAR 480 752 5.3e-8 PFAM
Pfam:7tm_2 481 721 7.5e-67 PFAM
low complexity region 753 763 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000109810
AA Change: I417T

PolyPhen 2 Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000105435
Gene: ENSMUSG00000005481
AA Change: I417T

DomainStartEndE-ValueType
low complexity region 5 18 N/A INTRINSIC
DEXDc 63 264 4.06e-54 SMART
HELICc 300 381 9.09e-25 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000140521
SMART Domains Protein: ENSMUSP00000116101
Gene: ENSMUSG00000005481

DomainStartEndE-ValueType
low complexity region 5 18 N/A INTRINSIC
DEXDc 63 208 2.82e-21 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000166939
SMART Domains Protein: ENSMUSP00000128220
Gene: ENSMUSG00000002885

DomainStartEndE-ValueType
signal peptide 1 21 N/A INTRINSIC
EGF 28 66 1.63e1 SMART
EGF_CA 67 117 5.92e-8 SMART
EGF_CA 118 165 1.78e-11 SMART
GPS 382 428 2.18e-8 SMART
Pfam:Dicty_CAR 429 701 2.1e-7 PFAM
Pfam:7tm_2 430 670 1.7e-66 PFAM
low complexity region 702 712 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000172396
AA Change: I417T

PolyPhen 2 Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000132222
Gene: ENSMUSG00000005481
AA Change: I417T

DomainStartEndE-ValueType
low complexity region 5 18 N/A INTRINSIC
DEXDc 63 264 4.06e-54 SMART
HELICc 300 381 9.09e-25 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000212949
AA Change: I417T

PolyPhen 2 Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.7%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the DEAD box protein family. These proteins are characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD) and are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure, such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of the DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene is thought to play a role in the prognosis of patients with gastrointestinal stromal tumors. A pseudogene of this gene is present on chromosome 13. Alternate splicing results in multiple transcript variants. Additional alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Sep 2013]
Allele List at MGI
Other mutations in this stock
Total: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik C T 3: 137,770,930 (GRCm39) Q40* probably null Het
1700034E13Rik T C 18: 52,796,705 (GRCm39) V81A probably damaging Het
A630089N07Rik A G 16: 97,866,855 (GRCm39) I369T probably benign Het
Aatk T A 11: 119,901,294 (GRCm39) Q977L probably benign Het
Abca4 A T 3: 121,928,844 (GRCm39) Q144H probably damaging Het
Ampd3 T C 7: 110,401,753 (GRCm39) F416L probably benign Het
Anks1b A G 10: 90,096,516 (GRCm39) E425G probably damaging Het
Atm A G 9: 53,393,730 (GRCm39) S1737P possibly damaging Het
Bsph1 T A 7: 13,204,255 (GRCm39) probably null Het
Cabyr C T 18: 12,887,154 (GRCm39) P262S probably benign Het
Cdc14a G A 3: 116,122,325 (GRCm39) P214L possibly damaging Het
Cep128 C A 12: 91,333,116 (GRCm39) probably null Het
Cfh T A 1: 140,075,487 (GRCm39) R250S probably damaging Het
Dgka T A 10: 128,558,408 (GRCm39) K548M probably damaging Het
Efr3a G A 15: 65,701,679 (GRCm39) V198I probably benign Het
Elapor1 T C 3: 108,389,654 (GRCm39) E203G probably damaging Het
Epg5 C T 18: 78,056,106 (GRCm39) T1760I probably damaging Het
Fat1 T C 8: 45,488,635 (GRCm39) V3472A possibly damaging Het
Fbxo48 T A 11: 16,903,402 (GRCm39) N9K probably benign Het
Fcgbpl1 T A 7: 27,846,560 (GRCm39) I1084N probably damaging Het
Fer1l6 A T 15: 58,466,727 (GRCm39) H833L probably damaging Het
Foxn1 G T 11: 78,251,786 (GRCm39) Q482K probably benign Het
Fstl5 A G 3: 76,615,162 (GRCm39) D741G probably damaging Het
Gmip C T 8: 70,270,641 (GRCm39) Q55* probably null Het
H2-T5 T C 17: 36,478,965 (GRCm39) N95D possibly damaging Het
Hapln2 G A 3: 87,929,958 (GRCm39) T306M possibly damaging Het
Kat6a T A 8: 23,428,676 (GRCm39) S1344T probably benign Het
Kctd1 C T 18: 15,119,401 (GRCm39) D705N possibly damaging Het
Lhx9 ACC ACCC 1: 138,769,544 (GRCm39) probably null Het
Micall2 G T 5: 139,701,548 (GRCm39) A482D possibly damaging Het
Mindy3 T A 2: 12,424,063 (GRCm39) M1L possibly damaging Het
Mtdh A G 15: 34,136,867 (GRCm39) E352G probably damaging Het
Muc5ac G A 7: 141,370,644 (GRCm39) V3219I probably benign Het
Myh4 A G 11: 67,143,794 (GRCm39) probably null Het
Ncor1 A G 11: 62,234,071 (GRCm39) I377T probably damaging Het
Oog4 C A 4: 143,165,679 (GRCm39) C156F possibly damaging Het
Or5m9 A T 2: 85,876,948 (GRCm39) I41F probably benign Het
Pcyt1a T C 16: 32,288,938 (GRCm39) S260P probably damaging Het
Phf3 A T 1: 30,843,711 (GRCm39) F1749L probably damaging Het
Prickle2 T C 6: 92,353,525 (GRCm39) D647G probably benign Het
Raver2 T C 4: 100,990,787 (GRCm39) S387P probably benign Het
Relch T C 1: 105,681,320 (GRCm39) L1184P probably damaging Het
Rgs19 A G 2: 181,330,941 (GRCm39) S231P possibly damaging Het
Rpl8 G T 15: 76,790,149 (GRCm39) R198L probably benign Het
Sacs T A 14: 61,416,737 (GRCm39) S77T possibly damaging Het
Samd14 G A 11: 94,912,280 (GRCm39) G219D probably damaging Het
Sec16a C T 2: 26,331,431 (GRCm39) V195M probably damaging Het
Sesn2 C T 4: 132,221,113 (GRCm39) V453I possibly damaging Het
Slc46a3 A T 5: 147,822,970 (GRCm39) C291S probably damaging Het
Smarcal1 A G 1: 72,630,332 (GRCm39) T129A possibly damaging Het
Sorl1 T A 9: 41,935,694 (GRCm39) R1041W possibly damaging Het
Sptlc3 T C 2: 139,408,506 (GRCm39) I207T probably benign Het
Srgap3 T C 6: 112,793,622 (GRCm39) D118G probably damaging Het
Tas2r117 T A 6: 132,779,892 (GRCm39) V10D probably benign Het
Tbcd A G 11: 121,500,206 (GRCm39) K1111E probably benign Het
Tor1aip1 A T 1: 155,911,566 (GRCm39) L139Q probably damaging Het
Trbv23 T C 6: 41,193,181 (GRCm39) V23A probably damaging Het
Ttll3 AAGTA AAGTATAGTA 6: 113,376,120 (GRCm39) probably null Het
Ttll3 GGCAAAG GGCAAAGCAAAG 6: 113,376,116 (GRCm39) probably null Het
Ttll3 CAAAGTAA CAAAGTAAAGTAA 6: 113,376,118 (GRCm39) probably null Het
Vmn1r42 T G 6: 89,821,769 (GRCm39) T267P possibly damaging Het
Vmn2r53 C A 7: 12,340,441 (GRCm39) V11F probably damaging Het
Vmn2r67 T C 7: 84,801,361 (GRCm39) M192V probably damaging Het
Vmn2r78 T C 7: 86,603,811 (GRCm39) V663A probably damaging Het
Zdhhc1 C T 8: 106,203,704 (GRCm39) G156S possibly damaging Het
Zfp318 AGAAG AGAAGAGGAAG 17: 46,723,464 (GRCm39) probably benign Het
Zfp318 GAAGAA GAAGAAAAAGAA 17: 46,723,459 (GRCm39) probably benign Het
Zfp318 AAGAAG AAGAAGTAGAAG 17: 46,723,460 (GRCm39) probably benign Het
Zfp560 A G 9: 20,259,339 (GRCm39) C508R probably damaging Het
Zfp654 G A 16: 64,606,961 (GRCm39) L414F probably damaging Het
Zfp872 A T 9: 22,111,355 (GRCm39) Y278F probably damaging Het
Zscan20 T C 4: 128,483,515 (GRCm39) S385G probably damaging Het
Other mutations in Ddx39a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02544:Ddx39a APN 8 84,449,402 (GRCm39) missense probably benign 0.03
IGL02712:Ddx39a APN 8 84,448,386 (GRCm39) missense probably benign 0.03
R0038:Ddx39a UTSW 8 84,449,127 (GRCm39) missense probably damaging 1.00
R0038:Ddx39a UTSW 8 84,449,127 (GRCm39) missense probably damaging 1.00
R0051:Ddx39a UTSW 8 84,447,251 (GRCm39) missense possibly damaging 0.83
R0051:Ddx39a UTSW 8 84,447,251 (GRCm39) missense possibly damaging 0.83
R0143:Ddx39a UTSW 8 84,447,179 (GRCm39) missense probably benign 0.22
R0147:Ddx39a UTSW 8 84,449,105 (GRCm39) missense possibly damaging 0.74
R0148:Ddx39a UTSW 8 84,449,105 (GRCm39) missense possibly damaging 0.74
R0392:Ddx39a UTSW 8 84,448,366 (GRCm39) missense probably damaging 0.97
R0426:Ddx39a UTSW 8 84,448,398 (GRCm39) missense probably benign 0.00
R0830:Ddx39a UTSW 8 84,446,452 (GRCm39) missense possibly damaging 0.47
R1509:Ddx39a UTSW 8 84,446,527 (GRCm39) missense probably damaging 1.00
R2935:Ddx39a UTSW 8 84,447,587 (GRCm39) missense possibly damaging 0.57
R3082:Ddx39a UTSW 8 84,449,335 (GRCm39) missense possibly damaging 0.57
R4050:Ddx39a UTSW 8 84,448,863 (GRCm39) missense probably benign 0.00
R4647:Ddx39a UTSW 8 84,448,902 (GRCm39) missense probably benign 0.00
R4804:Ddx39a UTSW 8 84,447,724 (GRCm39) missense probably damaging 0.99
R5242:Ddx39a UTSW 8 84,448,440 (GRCm39) missense probably benign 0.01
R5268:Ddx39a UTSW 8 84,448,950 (GRCm39) missense probably benign 0.08
R6598:Ddx39a UTSW 8 84,449,556 (GRCm39) missense probably benign 0.03
R6805:Ddx39a UTSW 8 84,449,766 (GRCm39) missense probably damaging 1.00
R7326:Ddx39a UTSW 8 84,449,100 (GRCm39) missense probably benign 0.31
R7559:Ddx39a UTSW 8 84,447,595 (GRCm39) missense possibly damaging 0.82
R7803:Ddx39a UTSW 8 84,446,229 (GRCm39) critical splice donor site probably null
R8103:Ddx39a UTSW 8 84,451,105 (GRCm39) critical splice acceptor site probably null
R9187:Ddx39a UTSW 8 84,449,113 (GRCm39) missense probably benign
R9483:Ddx39a UTSW 8 84,448,916 (GRCm39) missense probably benign 0.14
R9631:Ddx39a UTSW 8 84,447,729 (GRCm39) missense possibly damaging 0.92
X0026:Ddx39a UTSW 8 84,448,959 (GRCm39) missense probably benign 0.03
Predicted Primers PCR Primer
(F):5'- GAGGACTCAGACACCTACCTTC -3'
(R):5'- AGGTTCTGAAGCAGCAGGTG -3'

Sequencing Primer
(F):5'- TACCTTCACCGAGTGAGCG -3'
(R):5'- TGGGAAAGAGAGTGGCCATGTTG -3'
Posted On 2018-09-12