Mutagenetix > Incidental Mutation

Incidental Mutation 'R0147:Ddx39'

60834

Institutional Source

Beutler Lab

Gene Symbol

Ddx39

Ensembl Gene

ENSMUSG00000005481

Gene Name

DEAD (Asp-Glu-Ala-Asp) box polypeptide 39

Synonyms

2610307C23Rik, BAT1

MMRRC Submission

038431-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.913) question?

Stock #

R0147 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

83715177-83726892 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 83722476 bp (GRCm38)

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] [ENSMUST00000140521] [ENSMUST00000166939] [ENSMUST00000172396] [ENSMUST00000212949]

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

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

noncoding transcript
Transcript: ENSMUST00000140606

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

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: ENSMUST00000184114

Meta Mutation Damage Score

0.8889

Coding Region Coverage

1x: 98.9%
3x: 98.0%
10x: 94.5%
20x: 86.1%

Validation Efficiency

67% (88/131)

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: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3110002H16Rik	C	T	18: 12,189,271	R594C	probably damaging	Het
A2m	T	C	6: 121,662,446		probably null	Het
Abtb2	A	G	2: 103,567,135	I137V	probably benign	Het
Ank1	T	A	8: 23,123,977	N1545K	probably damaging	Het
Arl6	T	C	16: 59,618,790		probably benign	Het
Avl9	T	A	6: 56,736,502	D248E	probably benign	Het
Becn1	T	C	11: 101,301,736	E40G	probably damaging	Het
Bod1l	G	T	5: 41,818,697	A1758E	possibly damaging	Het
Btbd16	C	T	7: 130,779,594	T19I	probably damaging	Het
Casc3	T	A	11: 98,822,499	N246K	possibly damaging	Het
Celf1	G	T	2: 91,004,690		probably benign	Het
Chrm3	G	T	13: 9,878,744	N85K	probably damaging	Het
Cluh	T	A	11: 74,665,938	Y935N	probably damaging	Het
Col1a2	G	A	6: 4,518,822		probably benign	Het
Col6a5	T	C	9: 105,925,794	D1324G	unknown	Het
Ctcfl	T	C	2: 173,118,547	D81G	possibly damaging	Het
D630003M21Rik	C	T	2: 158,203,067		probably benign	Het
Dnmt3b	T	G	2: 153,661,457	N9K	possibly damaging	Het
Dock8	T	C	19: 25,119,459	L577P	probably benign	Het
Drc1	A	T	5: 30,281,489	N13I	possibly damaging	Het
Eml4	T	A	17: 83,421,652	N85K	probably damaging	Het
Epb41l4a	T	C	18: 33,798,800	T581A	probably damaging	Het
Epha3	T	C	16: 63,612,944	D446G	possibly damaging	Het
Fam208a	A	G	14: 27,471,768	D975G	probably benign	Het
Fam209	G	T	2: 172,473,980	G92C	probably damaging	Het
Fam98c	T	A	7: 29,152,721	R340*	probably null	Het
Fbxw10	T	G	11: 62,847,481		probably null	Het
Galr1	A	G	18: 82,405,570	L194P	probably benign	Het
Gar1	T	C	3: 129,829,473	H89R	probably damaging	Het
Gbp4	T	A	5: 105,119,496	Y519F	probably benign	Het
Gm28042	T	A	2: 120,036,463	S196T	probably benign	Het
Grid2	T	C	6: 64,533,587	Y734H	probably benign	Het
Grm6	T	A	11: 50,859,317	I466N	possibly damaging	Het
Hectd3	T	C	4: 116,997,040		probably benign	Het
Hpse2	A	C	19: 42,931,660		probably null	Het
Hspb7	T	C	4: 141,423,991	I148T	probably damaging	Het
Htr1d	C	A	4: 136,443,477	T339K	probably damaging	Het
Ip6k1	T	A	9: 108,045,894	D408E	probably damaging	Het
Irs2	A	T	8: 11,007,568	M288K	probably damaging	Het
Kansl3	A	T	1: 36,353,816	C225S	probably damaging	Het
Knop1	C	A	7: 118,845,838	R301L	probably benign	Het
Lama5	T	C	2: 180,190,406	H1714R	probably benign	Het
Mettl14	G	A	3: 123,371,394	T316I	probably damaging	Het
Mmp15	A	T	8: 95,372,317	N591Y	probably benign	Het
Mprip	T	A	11: 59,737,073	D93E	possibly damaging	Het
Mtmr14	T	A	6: 113,260,666		probably benign	Het
Muc5ac	T	C	7: 141,811,039	S1917P	probably benign	Het
Muc6	C	T	7: 141,651,990	C75Y	probably damaging	Het
Naip1	A	T	13: 100,426,910	H582Q	possibly damaging	Het
Nbeal2	G	A	9: 110,642,143	R264*	probably null	Het
Neb	T	C	2: 52,249,376	K140E	probably damaging	Het
Nfya	A	G	17: 48,398,998	V48A	possibly damaging	Het
Ngf	G	T	3: 102,509,803		probably benign	Het
Nsmce2	T	G	15: 59,378,957	S26A	probably damaging	Het
Olfr1026	T	A	2: 85,924,018	I250N	possibly damaging	Het
Olfr601	T	C	7: 103,358,406	T263A	possibly damaging	Het
Olfr873	T	G	9: 20,301,091	M297R	probably damaging	Het
Pax1	A	G	2: 147,373,734	S424G	probably benign	Het
Pcdhb19	A	T	18: 37,497,182	Q10L	probably benign	Het
Pdcl	T	C	2: 37,352,130	I203V	probably benign	Het
Pknox1	T	A	17: 31,604,790	N379K	probably benign	Het
Plxna1	C	T	6: 89,320,710	A1831T	possibly damaging	Het
Prodh	T	G	16: 18,077,813	Q360P	probably damaging	Het
Pygo2	T	C	3: 89,433,303	V299A	probably damaging	Het
Raf1	C	T	6: 115,632,973	G202S	probably benign	Het
Rgs11	T	A	17: 26,207,459		probably null	Het
Rnf13	A	G	3: 57,802,468	D144G	probably damaging	Het
Rtel1	T	C	2: 181,321,046	C31R	probably damaging	Het
Rubcnl	T	A	14: 75,042,458	I427K	probably damaging	Het
Sec23ip	C	T	7: 128,779,051		probably benign	Het
Slc25a26	T	A	6: 94,592,526		probably null	Het
Slc6a7	A	G	18: 61,002,111		probably benign	Het
Slco6b1	A	T	1: 96,987,837		noncoding transcript	Het
Spata17	A	G	1: 187,112,601	V111A	probably damaging	Het
Spata22	T	A	11: 73,331,153	M1K	probably null	Het
Svep1	C	T	4: 58,116,608	D881N	possibly damaging	Het
Sypl2	T	A	3: 108,219,095	N67I	possibly damaging	Het
Tenm3	T	C	8: 48,236,720	Y1944C	probably damaging	Het
Tm9sf4	G	T	2: 153,195,313	V365L	probably benign	Het
Tmc3	T	C	7: 83,607,742	V401A	probably damaging	Het
Trpm2	C	T	10: 77,925,825	G997D	probably damaging	Het
Unc5b	A	T	10: 60,772,297	S675T	probably damaging	Het
Vmn1r217	A	G	13: 23,113,937	M265T	probably benign	Het
Vps54	T	A	11: 21,300,259	D548E	probably benign	Het
Wdfy3	A	G	5: 101,917,411	V1297A	probably benign	Het
Wdr46	T	A	17: 33,941,023	F70I	probably benign	Het
Zdbf2	C	T	1: 63,304,006	Q515*	probably null	Het
Zfp710	T	A	7: 80,081,973	C299*	probably null	Het

Other mutations in Ddx39

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02544:Ddx39	APN	8	83722773	missense	probably benign	0.03
IGL02712:Ddx39	APN	8	83721757	missense	probably benign	0.03
R0038:Ddx39	UTSW	8	83722498	missense	probably damaging	1.00
R0038:Ddx39	UTSW	8	83722498	missense	probably damaging	1.00
R0051:Ddx39	UTSW	8	83720622	missense	possibly damaging	0.83
R0051:Ddx39	UTSW	8	83720622	missense	possibly damaging	0.83
R0143:Ddx39	UTSW	8	83720550	missense	probably benign	0.22
R0148:Ddx39	UTSW	8	83722476	missense	possibly damaging	0.74
R0392:Ddx39	UTSW	8	83721737	missense	probably damaging	0.97
R0426:Ddx39	UTSW	8	83721769	missense	probably benign	0.00
R0830:Ddx39	UTSW	8	83719823	missense	possibly damaging	0.47
R1509:Ddx39	UTSW	8	83719898	missense	probably damaging	1.00
R2935:Ddx39	UTSW	8	83720958	missense	possibly damaging	0.57
R3082:Ddx39	UTSW	8	83722706	missense	possibly damaging	0.57
R4050:Ddx39	UTSW	8	83722234	missense	probably benign	0.00
R4647:Ddx39	UTSW	8	83722273	missense	probably benign	0.00
R4804:Ddx39	UTSW	8	83721095	missense	probably damaging	0.99
R5242:Ddx39	UTSW	8	83721811	missense	probably benign	0.01
R5268:Ddx39	UTSW	8	83722321	missense	probably benign	0.08
R6598:Ddx39	UTSW	8	83722927	missense	probably benign	0.03
R6805:Ddx39	UTSW	8	83723137	missense	probably damaging	1.00
R6852:Ddx39	UTSW	8	83723017	missense	probably benign	0.03
R7326:Ddx39	UTSW	8	83722471	missense	probably benign	0.31
R7559:Ddx39	UTSW	8	83720966	missense	possibly damaging	0.82
R7803:Ddx39	UTSW	8	83719600	critical splice donor site	probably null
R8103:Ddx39	UTSW	8	83724476	critical splice acceptor site	probably null
R9187:Ddx39	UTSW	8	83722484	missense	probably benign
R9483:Ddx39	UTSW	8	83722287	missense	probably benign	0.14
R9631:Ddx39	UTSW	8	83721100	missense	possibly damaging	0.92
X0026:Ddx39	UTSW	8	83722330	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