Mutagenetix > Incidental Mutation

Incidental Mutation 'R0148:Ddx39a'

60878

Institutional Source

Beutler Lab

Gene Symbol

Ddx39a

Ensembl Gene

ENSMUSG00000005481

Gene Name

DEAD box helicase 39a

Synonyms

BAT1, 2610307C23Rik, Ddx39

MMRRC Submission

038432-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.940) question?

Stock #

R0148 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

84441806-84453521 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 84449105 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Cysteine at position 298 (R298C)

Ref Sequence

ENSEMBL: ENSMUSP00000148329 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000002964] [ENSMUST00000019576] [ENSMUST00000075843] [ENSMUST00000109802] [ENSMUST00000109810] [ENSMUST00000172396] [ENSMUST00000212949] [ENSMUST00000140521] [ENSMUST00000166939]

AlphaFold

Q8VDW0

Predicted Effect

probably benign
Transcript: ENSMUST00000002964

SMART Domains

Protein: ENSMUSP00000002964
Gene: ENSMUSG00000002885

Domain	Start	End	E-Value	Type
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

possibly damaging
Transcript: ENSMUST00000019576
AA Change: R298C

PolyPhen 2 Score 0.742 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000019576
Gene: ENSMUSG00000005481
AA Change: R298C

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
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

possibly damaging
Transcript: ENSMUST00000109810
AA Change: R298C

PolyPhen 2 Score 0.742 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000105435
Gene: ENSMUSG00000005481
AA Change: R298C

Domain	Start	End	E-Value	Type
low complexity region	5	18	N/A	INTRINSIC
DEXDc	63	264	4.06e-54	SMART
HELICc	300	381	9.09e-25	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127505

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138789

Predicted Effect

possibly damaging
Transcript: ENSMUST00000172396
AA Change: R298C

PolyPhen 2 Score 0.742 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000132222
Gene: ENSMUSG00000005481
AA Change: R298C

Domain	Start	End	E-Value	Type
low complexity region	5	18	N/A	INTRINSIC
DEXDc	63	264	4.06e-54	SMART
HELICc	300	381	9.09e-25	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000212949
AA Change: R298C

PolyPhen 2 Score 0.742 (Sensitivity: 0.85; Specificity: 0.92)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000140606

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184114

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139797

Predicted Effect

probably benign
Transcript: ENSMUST00000140521

SMART Domains

Protein: ENSMUSP00000116101
Gene: ENSMUSG00000005481

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
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

Meta Mutation Damage Score

0.8889

Coding Region Coverage

1x: 99.0%
3x: 98.1%
10x: 96.0%
20x: 91.8%

Validation Efficiency

86% (30/35)

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: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2m	T	C	6: 121,639,405 (GRCm39)		probably null	Het
Agtr1a	T	C	13: 30,565,927 (GRCm39)	S331P	probably benign	Het
Ank1	T	A	8: 23,613,993 (GRCm39)	N1545K	probably damaging	Het
Bahcc1	A	T	11: 120,159,230 (GRCm39)	Q152H	probably damaging	Het
Bend3	T	A	10: 43,387,946 (GRCm39)	Y780N	probably damaging	Het
Bod1l	G	T	5: 41,976,040 (GRCm39)	A1758E	possibly damaging	Het
Ctcfl	T	C	2: 172,960,340 (GRCm39)	D81G	possibly damaging	Het
Dock8	T	C	19: 25,096,823 (GRCm39)	L577P	probably benign	Het
Drc1	A	T	5: 30,486,487 (GRCm39)	N13I	possibly damaging	Het
Efl1	T	C	7: 82,320,878 (GRCm39)	S104P	probably damaging	Het
Eml4	T	A	17: 83,729,081 (GRCm39)	N85K	probably damaging	Het
Epb41l4a	T	C	18: 33,931,853 (GRCm39)	T581A	probably damaging	Het
Epha3	T	C	16: 63,433,307 (GRCm39)	D446G	possibly damaging	Het
Fam209	G	T	2: 172,315,900 (GRCm39)	G92C	probably damaging	Het
Fbln1	G	A	15: 85,115,027 (GRCm39)	R193H	probably damaging	Het
Fbxw21	A	G	9: 108,977,085 (GRCm39)		probably null	Het
Fgf17	C	T	14: 70,876,313 (GRCm39)	R49Q	probably damaging	Het
Flnb	T	C	14: 7,939,077 (GRCm38)	S2307P	probably benign	Het
Galr1	A	G	18: 82,423,695 (GRCm39)	L194P	probably benign	Het
Gar1	T	C	3: 129,623,122 (GRCm39)	H89R	probably damaging	Het
Gbp4	T	A	5: 105,267,362 (GRCm39)	Y519F	probably benign	Het
Git1	A	G	11: 77,396,554 (GRCm39)	T601A	probably benign	Het
Gm10722	T	"C,A"	9: 3,001,405 (GRCm39)		probably null	Het
Gm5142	C	T	14: 59,416,119 (GRCm39)	R13H	possibly damaging	Het
Gria2	A	C	3: 80,615,038 (GRCm39)	W481G	probably damaging	Het
Homer2	T	C	7: 81,274,026 (GRCm39)	T57A	probably benign	Het
Hpse2	A	C	19: 42,920,099 (GRCm39)		probably null	Het
Hspb7	T	C	4: 141,151,302 (GRCm39)	I148T	probably damaging	Het
Htr1d	C	A	4: 136,170,788 (GRCm39)	T339K	probably damaging	Het
Il4ra	T	A	7: 125,174,709 (GRCm39)	C306S	probably damaging	Het
Kansl3	A	T	1: 36,392,897 (GRCm39)	C225S	probably damaging	Het
Lama3	G	A	18: 12,581,329 (GRCm39)	C596Y	probably damaging	Het
Lama5	T	C	2: 179,832,199 (GRCm39)	H1714R	probably benign	Het
Marchf6	C	T	15: 31,490,758 (GRCm39)	V293M	probably damaging	Het
Med12l	A	G	3: 58,945,075 (GRCm39)	D100G	probably damaging	Het
Mettl14	G	A	3: 123,165,043 (GRCm39)	T316I	probably damaging	Het
Mmp15	A	T	8: 96,098,945 (GRCm39)	N591Y	probably benign	Het
Mrpl53	T	C	6: 83,086,518 (GRCm39)	L74P	probably damaging	Het
Mvp	C	T	7: 126,589,037 (GRCm39)	V577M	probably damaging	Het
Neb	T	C	2: 52,139,388 (GRCm39)	K140E	probably damaging	Het
Nfya	A	G	17: 48,706,026 (GRCm39)	V48A	possibly damaging	Het
Ngf	G	T	3: 102,417,119 (GRCm39)		probably benign	Het
Nipsnap3b	C	T	4: 53,017,088 (GRCm39)	A104V	possibly damaging	Het
Nlrp14	A	G	7: 106,781,928 (GRCm39)	Y375C	probably benign	Het
Nod1	A	G	6: 54,915,202 (GRCm39)	Y764H	probably damaging	Het
Or13d1	A	T	4: 52,971,232 (GRCm39)	I204F	probably benign	Het
Or2w25	G	A	11: 59,504,320 (GRCm39)	V177M	probably damaging	Het
Or7e177	T	G	9: 20,212,387 (GRCm39)	M297R	probably damaging	Het
Pcdhb19	A	T	18: 37,630,235 (GRCm39)	Q10L	probably benign	Het
Pdcl	T	C	2: 37,242,142 (GRCm39)	I203V	probably benign	Het
Peg10	C	A	6: 4,755,711 (GRCm39)	R96S	possibly damaging	Het
Pknox1	T	A	17: 31,823,764 (GRCm39)	N379K	probably benign	Het
Prodh	T	G	16: 17,895,677 (GRCm39)	Q360P	probably damaging	Het
Raf1	C	T	6: 115,609,934 (GRCm39)	G202S	probably benign	Het
Rgs11	T	A	17: 26,426,433 (GRCm39)		probably null	Het
Rilp	A	T	11: 75,401,059 (GRCm39)	H29L	probably damaging	Het
Rtel1	T	C	2: 180,962,839 (GRCm39)	C31R	probably damaging	Het
Rubcnl	T	A	14: 75,279,898 (GRCm39)	I427K	probably damaging	Het
Ryr1	C	A	7: 28,751,460 (GRCm39)	R3706L	probably damaging	Het
Ryr2	T	C	13: 11,729,434 (GRCm39)	D2396G	probably damaging	Het
Slc45a2	T	C	15: 11,025,954 (GRCm39)	S435P	probably damaging	Het
Spata17	A	G	1: 186,844,798 (GRCm39)	V111A	probably damaging	Het
Svep1	C	T	4: 58,116,608 (GRCm39)	D881N	possibly damaging	Het
Sypl2	T	A	3: 108,126,411 (GRCm39)	N67I	possibly damaging	Het
Tenm3	T	C	8: 48,689,755 (GRCm39)	Y1944C	probably damaging	Het
Tep1	A	T	14: 51,062,246 (GRCm39)	D2535E	possibly damaging	Het
Tkt	T	A	14: 30,294,177 (GRCm39)	I529N	probably damaging	Het
Trp53i11	T	G	2: 93,028,080 (GRCm39)	V39G	probably damaging	Het
Trpm2	C	T	10: 77,761,659 (GRCm39)	G997D	probably damaging	Het
Usp3	A	G	9: 66,447,449 (GRCm39)	V219A	possibly damaging	Het
Usp4	T	A	9: 108,268,870 (GRCm39)		probably null	Het
Wdfy3	A	G	5: 102,065,277 (GRCm39)	V1297A	probably benign	Het
Wdr46	T	A	17: 34,159,997 (GRCm39)	F70I	probably benign	Het
Xkr6	T	C	14: 64,056,998 (GRCm39)	V303A	unknown	Het
Zdbf2	C	T	1: 63,343,165 (GRCm39)	Q515*	probably null	Het
Zfhx2	A	G	14: 55,310,354 (GRCm39)	Y731H	possibly damaging	Het

Other mutations in Ddx39a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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
R6852:Ddx39a	UTSW	8	84,449,646 (GRCm39)	missense	probably benign	0.03
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'- AGAACCGTAAGCTCTTCGACCTCC -3'
(R):5'- TGCCAAACAGATTAGTAGCCACCAG -3'

Sequencing Primer
(F):5'- CTCGACGTGCTAGAGTTTAACC -3'
(R):5'- GATTAGTAGCCACCAGGATTCGTC -3'

Posted On

2013-07-24