Mutagenetix > Incidental Mutation

Incidental Mutation 'R1460:Dhx9'

162021

Institutional Source

Beutler Lab

Gene Symbol

Dhx9

Ensembl Gene

ENSMUSG00000042699

Gene Name

DExH-box helicase 9

Synonyms

Ddx9, NDHII, nuclear DNA helicase II, leukophysin, NDH II, RNA helicase, RHA

MMRRC Submission

039515-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1460 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

153331504-153363406 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 153341426 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 607 (D607E)

Ref Sequence

ENSEMBL: ENSMUSP00000038135 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000042141] [ENSMUST00000186380] [ENSMUST00000186966] [ENSMUST00000188345]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000042141
AA Change: D607E

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000038135
Gene: ENSMUSG00000042699
AA Change: D607E

Domain	Start	End	E-Value	Type
DSRM	4	70	2.23e-17	SMART
low complexity region	80	91	N/A	INTRINSIC
low complexity region	93	120	N/A	INTRINSIC
DSRM	184	254	3.52e-15	SMART
low complexity region	284	299	N/A	INTRINSIC
low complexity region	334	349	N/A	INTRINSIC
DEXDc	389	576	1.61e-25	SMART
low complexity region	592	608	N/A	INTRINSIC
HELICc	667	772	4.69e-18	SMART
HA2	834	922	1.33e-24	SMART
Pfam:OB_NTP_bind	961	1077	1.6e-18	PFAM
low complexity region	1173	1309	N/A	INTRINSIC
low complexity region	1313	1337	N/A	INTRINSIC
low complexity region	1339	1384	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000186380
AA Change: D606E

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000139825
Gene: ENSMUSG00000042699
AA Change: D606E

Domain	Start	End	E-Value	Type
DSRM	4	70	1.3e-19	SMART
low complexity region	80	91	N/A	INTRINSIC
low complexity region	93	120	N/A	INTRINSIC
DSRM	183	253	2.1e-17	SMART
low complexity region	283	298	N/A	INTRINSIC
low complexity region	333	348	N/A	INTRINSIC
DEXDc	388	575	6.6e-28	SMART
low complexity region	591	607	N/A	INTRINSIC
HELICc	666	771	1.9e-20	SMART
HA2	833	921	9.9e-29	SMART
Pfam:OB_NTP_bind	960	1076	5e-13	PFAM
low complexity region	1172	1308	N/A	INTRINSIC
low complexity region	1312	1336	N/A	INTRINSIC
low complexity region	1338	1383	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000186966

SMART Domains

Protein: ENSMUSP00000139806
Gene: ENSMUSG00000042699

Domain	Start	End	E-Value	Type
DSRM	4	70	1.3e-19	SMART
low complexity region	80	91	N/A	INTRINSIC
low complexity region	93	120	N/A	INTRINSIC
DSRM	183	253	2.1e-17	SMART
low complexity region	283	298	N/A	INTRINSIC
low complexity region	333	348	N/A	INTRINSIC
Blast:DEXDc	349	451	1e-37	BLAST
PDB:3LLM\|B	349	456	2e-55	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000188345
AA Change: D607E

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000139827
Gene: ENSMUSG00000042699
AA Change: D607E

Domain	Start	End	E-Value	Type
DSRM	4	70	1.3e-19	SMART
low complexity region	80	91	N/A	INTRINSIC
low complexity region	93	120	N/A	INTRINSIC
DSRM	184	254	2.1e-17	SMART
low complexity region	284	299	N/A	INTRINSIC
low complexity region	334	349	N/A	INTRINSIC
DEXDc	389	576	6.6e-28	SMART
low complexity region	592	608	N/A	INTRINSIC
Pfam:Helicase_C	678	735	6.4e-9	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000190544

Meta Mutation Damage Score

0.0584

Coding Region Coverage

1x: 98.9%
3x: 98.0%
10x: 95.2%
20x: 89.1%

Validation Efficiency

94% (93/99)

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 DEAH-containing family of RNA helicases. The encoded protein is an enzyme that catalyzes the ATP-dependent unwinding of double-stranded RNA and DNA-RNA complexes. This protein localizes to both the nucleus and the cytoplasm and functions as a transcriptional regulator. This protein may also be involved in the expression and nuclear export of retroviral RNAs. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 11 and 13.[provided by RefSeq, Feb 2010]
PHENOTYPE: Homozygotes die in embryonic stages with massive apoptotic cell death in embryonic ectodermal cells. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 96 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930522H14Rik	A	T	4: 109,388,407 (GRCm39)		probably null	Het
Abcb11	A	G	2: 69,087,718 (GRCm39)		probably benign	Het
Abi3bp	T	C	16: 56,382,780 (GRCm39)	V130A	probably damaging	Het
Adamts4	A	G	1: 171,084,009 (GRCm39)		probably benign	Het
Adgrd1	A	G	5: 129,199,627 (GRCm39)	T155A	possibly damaging	Het
Ano3	A	T	2: 110,513,103 (GRCm39)	S631T	probably damaging	Het
Ass1	G	A	2: 31,404,753 (GRCm39)	V345I	probably benign	Het
Atg7	G	A	6: 114,680,325 (GRCm39)	A384T	probably damaging	Het
Atp6v0a1	T	A	11: 100,924,824 (GRCm39)	I303N	probably damaging	Het
B3gntl1	T	G	11: 121,530,624 (GRCm39)	Y149S	probably damaging	Het
Btnl2	A	G	17: 34,585,424 (GRCm39)	D475G	probably benign	Het
Cdcp1	A	T	9: 123,009,092 (GRCm39)	S529T	possibly damaging	Het
Cenpt	A	G	8: 106,575,520 (GRCm39)	L194P	probably damaging	Het
Cfhr4	T	A	1: 139,625,934 (GRCm39)	I788F	probably damaging	Het
Chmp4b	A	G	2: 154,534,515 (GRCm39)	D177G	possibly damaging	Het
Chmp7	C	T	14: 69,956,899 (GRCm39)	M336I	probably benign	Het
Cish	G	T	9: 107,177,596 (GRCm39)	E91*	probably null	Het
Col22a1	T	C	15: 71,693,780 (GRCm39)	D740G	unknown	Het
Cplane2	T	C	4: 140,945,523 (GRCm39)	F125L	probably damaging	Het
Crocc	G	A	4: 140,756,551 (GRCm39)	Q1025*	probably null	Het
Ctrc	C	A	4: 141,566,120 (GRCm39)		probably benign	Het
Cyb5r2	T	A	7: 107,356,450 (GRCm39)	D7V	probably benign	Het
Dhx29	T	C	13: 113,101,744 (GRCm39)		probably benign	Het
Dnajb7	C	T	15: 81,291,888 (GRCm39)	G150R	probably benign	Het
Dnase1l3	T	A	14: 7,974,050 (GRCm38)	T214S	probably benign	Het
Dpm1	A	T	2: 168,052,549 (GRCm39)	I229N	probably damaging	Het
Dstn	T	C	2: 143,780,408 (GRCm39)	V36A	possibly damaging	Het
Entpd1	T	C	19: 40,714,632 (GRCm39)	V247A	probably damaging	Het
Ephb3	C	A	16: 21,037,672 (GRCm39)	H277Q	probably benign	Het
Etl4	A	T	2: 20,793,288 (GRCm39)	N671I	probably damaging	Het
Fabp3	C	T	4: 130,206,180 (GRCm39)	T57I	probably benign	Het
Fancd2os	G	A	6: 113,574,973 (GRCm39)	T11I	probably damaging	Het
Fcrlb	G	T	1: 170,739,853 (GRCm39)		probably benign	Het
Fhip1a	T	C	3: 85,638,183 (GRCm39)	I39V	probably damaging	Het
Gm9991	T	C	1: 90,606,780 (GRCm39)		noncoding transcript	Het
Gstk1	C	T	6: 42,223,529 (GRCm39)	R40W	probably damaging	Het
Gstt1	C	T	10: 75,620,004 (GRCm39)	V190M	probably damaging	Het
Hectd2	G	A	19: 36,592,908 (GRCm39)	W691*	probably null	Het
Hecw2	T	C	1: 53,852,404 (GRCm39)	T1572A	probably damaging	Het
Hoxa5	T	C	6: 52,180,928 (GRCm39)	T135A	probably benign	Het
Igfl3	T	A	7: 17,913,880 (GRCm39)	C77S	possibly damaging	Het
Itgb4	A	G	11: 115,874,990 (GRCm39)	D449G	probably damaging	Het
Larp1b	T	C	3: 40,916,653 (GRCm39)	V11A	probably benign	Het
Lhx9	A	G	1: 138,766,447 (GRCm39)		probably benign	Het
Lig3	G	T	11: 82,686,624 (GRCm39)		probably benign	Het
Lipo4	A	C	19: 33,476,718 (GRCm39)	F343L	probably benign	Het
Lyn	T	A	4: 3,789,908 (GRCm39)	Y480*	probably null	Het
Mib2	C	T	4: 155,743,917 (GRCm39)	G42S	probably damaging	Het
Mill1	C	A	7: 17,996,595 (GRCm39)	A137D	probably damaging	Het
Mmut	T	C	17: 41,248,266 (GRCm39)	Y98H	probably damaging	Het
Morc2a	A	T	11: 3,633,794 (GRCm39)	R635S	probably benign	Het
Mpped2	A	G	2: 106,575,237 (GRCm39)		probably benign	Het
Mug2	T	C	6: 122,017,492 (GRCm39)		probably benign	Het
Mynn	C	A	3: 30,657,853 (GRCm39)	S57Y	probably damaging	Het
Myo3b	G	A	2: 70,062,798 (GRCm39)	E333K	probably benign	Het
Myt1	A	T	2: 181,444,725 (GRCm39)	I514F	probably damaging	Het
Nlrp4f	A	G	13: 65,338,082 (GRCm39)	C708R	probably benign	Het
Nod2	A	G	8: 89,390,440 (GRCm39)	E249G	probably damaging	Het
Npy2r	T	C	3: 82,448,251 (GRCm39)	I175V	probably benign	Het
Obscn	A	T	11: 58,946,792 (GRCm39)	V4114D	probably damaging	Het
Or1l8	A	T	2: 36,817,820 (GRCm39)	M102K	probably damaging	Het
Or2y12	T	A	11: 49,426,504 (GRCm39)	M164K	possibly damaging	Het
Or4a76	A	G	2: 89,460,282 (GRCm39)		probably null	Het
Or52e7	T	A	7: 104,684,915 (GRCm39)	I170N	possibly damaging	Het
Or8g33	A	G	9: 39,337,503 (GRCm39)	M288T	probably benign	Het
Pbxip1	T	A	3: 89,352,921 (GRCm39)	I196N	probably damaging	Het
Piezo1	G	A	8: 123,228,890 (GRCm39)	T209M	possibly damaging	Het
Polr1a	T	C	6: 71,918,368 (GRCm39)	M642T	probably damaging	Het
Prdm4	T	C	10: 85,743,686 (GRCm39)	M190V	probably benign	Het
Psmd7	G	A	8: 108,307,691 (GRCm39)	S264L	possibly damaging	Het
Qrich1	T	G	9: 108,410,846 (GRCm39)		probably benign	Het
Rapgef4	G	T	2: 71,861,520 (GRCm39)		probably null	Het
Rfx5	T	C	3: 94,863,636 (GRCm39)	I95T	probably damaging	Het
Rgr	G	A	14: 36,767,683 (GRCm39)	R113C	probably damaging	Het
Rnf20	T	C	4: 49,645,873 (GRCm39)		probably benign	Het
Rps3a1	G	A	3: 86,045,369 (GRCm39)	A241V	probably benign	Het
Rttn	A	T	18: 89,127,481 (GRCm39)		probably benign	Het
Scn2a	A	G	2: 65,532,187 (GRCm39)	T600A	probably damaging	Het
Scyl2	T	C	10: 89,493,751 (GRCm39)	D339G	possibly damaging	Het
Sipa1	T	A	19: 5,701,475 (GRCm39)	H1029L	probably benign	Het
Slc49a4	T	C	16: 35,539,736 (GRCm39)	T362A	probably benign	Het
Snrnp48	A	G	13: 38,395,081 (GRCm39)	T124A	probably benign	Het
Sptbn1	A	T	11: 30,088,637 (GRCm39)	M875K	possibly damaging	Het
Supt6	A	G	11: 78,113,024 (GRCm39)	V973A	possibly damaging	Het
Supv3l1	T	C	10: 62,279,162 (GRCm39)		probably benign	Het
Svep1	G	T	4: 58,068,740 (GRCm39)	N3015K	possibly damaging	Het
Tgfb3	A	G	12: 86,105,841 (GRCm39)		probably benign	Het
Trerf1	A	G	17: 47,628,771 (GRCm39)		noncoding transcript	Het
Trim24	T	A	6: 37,941,761 (GRCm39)	F904I	probably damaging	Het
Trim30d	T	A	7: 104,121,311 (GRCm39)	Y328F	probably benign	Het
Ttn	T	C	2: 76,698,717 (GRCm39)	E6G	probably damaging	Het
Ube2m	T	C	7: 12,769,762 (GRCm39)		probably benign	Het
Vmn2r-ps158	A	T	7: 42,672,639 (GRCm39)	R91S	probably benign	Het
Wdr90	A	T	17: 26,079,422 (GRCm39)	S237R	possibly damaging	Het
Zfp735	A	T	11: 73,603,159 (GRCm39)	H701L	possibly damaging	Het
Zp1	T	C	19: 10,896,242 (GRCm39)	D161G	probably benign	Het

Other mutations in Dhx9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00500:Dhx9	APN	1	153,341,494 (GRCm39)	missense	probably damaging	1.00
IGL01284:Dhx9	APN	1	153,340,644 (GRCm39)	missense	probably damaging	1.00
IGL01555:Dhx9	APN	1	153,335,312 (GRCm39)	missense	probably damaging	1.00
IGL01767:Dhx9	APN	1	153,344,614 (GRCm39)	splice site	probably benign
IGL02938:Dhx9	APN	1	153,340,376 (GRCm39)	missense	probably benign	0.37
R0001:Dhx9	UTSW	1	153,338,382 (GRCm39)	missense	probably damaging	1.00
R0046:Dhx9	UTSW	1	153,348,453 (GRCm39)	missense	probably benign	0.27
R0309:Dhx9	UTSW	1	153,341,441 (GRCm39)	missense	probably benign	0.00
R0517:Dhx9	UTSW	1	153,354,662 (GRCm39)	missense	possibly damaging	0.93
R0589:Dhx9	UTSW	1	153,348,037 (GRCm39)	missense	probably damaging	1.00
R1217:Dhx9	UTSW	1	153,334,109 (GRCm39)	missense	probably damaging	1.00
R1406:Dhx9	UTSW	1	153,340,684 (GRCm39)	missense	probably damaging	1.00
R1406:Dhx9	UTSW	1	153,340,684 (GRCm39)	missense	probably damaging	1.00
R1430:Dhx9	UTSW	1	153,359,493 (GRCm39)	missense	probably benign	0.44
R1456:Dhx9	UTSW	1	153,341,441 (GRCm39)	missense	probably benign	0.00
R1724:Dhx9	UTSW	1	153,334,234 (GRCm39)	missense	probably benign	0.00
R1848:Dhx9	UTSW	1	153,341,499 (GRCm39)	missense	probably damaging	0.99
R1922:Dhx9	UTSW	1	153,336,020 (GRCm39)	splice site	probably null
R2001:Dhx9	UTSW	1	153,331,857 (GRCm39)	nonsense	probably null
R3084:Dhx9	UTSW	1	153,341,445 (GRCm39)	missense	probably benign	0.34
R3085:Dhx9	UTSW	1	153,341,445 (GRCm39)	missense	probably benign	0.34
R3123:Dhx9	UTSW	1	153,341,452 (GRCm39)	missense	possibly damaging	0.90
R3730:Dhx9	UTSW	1	153,353,866 (GRCm39)	missense	probably benign	0.16
R4274:Dhx9	UTSW	1	153,344,672 (GRCm39)	missense	probably damaging	1.00
R4353:Dhx9	UTSW	1	153,347,535 (GRCm39)	missense	probably damaging	1.00
R4560:Dhx9	UTSW	1	153,342,903 (GRCm39)	missense	probably damaging	1.00
R4583:Dhx9	UTSW	1	153,336,049 (GRCm39)	missense	probably damaging	0.98
R4598:Dhx9	UTSW	1	153,342,797 (GRCm39)	frame shift	probably null
R4603:Dhx9	UTSW	1	153,342,797 (GRCm39)	frame shift	probably null
R4889:Dhx9	UTSW	1	153,356,895 (GRCm39)	missense	probably damaging	1.00
R4931:Dhx9	UTSW	1	153,348,419 (GRCm39)	missense	probably benign	0.02
R5411:Dhx9	UTSW	1	153,356,969 (GRCm39)	missense	probably benign	0.27
R5569:Dhx9	UTSW	1	153,342,838 (GRCm39)	missense	possibly damaging	0.83
R5635:Dhx9	UTSW	1	153,359,493 (GRCm39)	missense	probably benign	0.44
R5659:Dhx9	UTSW	1	153,347,481 (GRCm39)	missense	probably damaging	1.00
R6128:Dhx9	UTSW	1	153,353,835 (GRCm39)	missense	probably damaging	1.00
R6215:Dhx9	UTSW	1	153,348,209 (GRCm39)	missense	probably damaging	1.00
R6428:Dhx9	UTSW	1	153,332,324 (GRCm39)	unclassified	probably benign
R6489:Dhx9	UTSW	1	153,332,389 (GRCm39)	unclassified	probably benign
R6717:Dhx9	UTSW	1	153,349,210 (GRCm39)	splice site	probably null
R7098:Dhx9	UTSW	1	153,340,768 (GRCm39)	missense	probably benign
R7209:Dhx9	UTSW	1	153,340,369 (GRCm39)	missense	possibly damaging	0.90
R7226:Dhx9	UTSW	1	153,341,423 (GRCm39)	missense	probably benign	0.00
R7440:Dhx9	UTSW	1	153,356,977 (GRCm39)	missense	probably benign
R7685:Dhx9	UTSW	1	153,334,152 (GRCm39)	missense	probably damaging	0.99
R7712:Dhx9	UTSW	1	153,340,747 (GRCm39)	missense	probably benign	0.07
R8088:Dhx9	UTSW	1	153,338,443 (GRCm39)	missense	probably benign	0.26
R8371:Dhx9	UTSW	1	153,331,961 (GRCm39)	missense	unknown
R8397:Dhx9	UTSW	1	153,344,657 (GRCm39)	missense	probably damaging	1.00
R8502:Dhx9	UTSW	1	153,335,210 (GRCm39)	missense	probably benign	0.01
R8519:Dhx9	UTSW	1	153,348,922 (GRCm39)	missense	probably damaging	1.00
R8531:Dhx9	UTSW	1	153,334,182 (GRCm39)	missense	possibly damaging	0.95
R8842:Dhx9	UTSW	1	153,338,335 (GRCm39)	missense	possibly damaging	0.91
R9145:Dhx9	UTSW	1	153,336,826 (GRCm39)	missense	probably damaging	1.00
R9295:Dhx9	UTSW	1	153,340,673 (GRCm39)	missense	probably damaging	0.98
R9557:Dhx9	UTSW	1	153,333,292 (GRCm39)	missense	probably benign	0.10
R9661:Dhx9	UTSW	1	153,340,393 (GRCm39)	missense	probably damaging	1.00
X0066:Dhx9	UTSW	1	153,348,275 (GRCm39)	missense	probably benign	0.00
Z1177:Dhx9	UTSW	1	153,332,321 (GRCm39)	missense	unknown

Predicted Primers

PCR Primer
(F):5'- TTTTCCAGGTACTCTGACATACAGCAAC -3'
(R):5'- TGGCAAGGGAGCACAGCTTAAC -3'

Sequencing Primer
(F):5'- GAGTATATAACCTCAACAGTTCCATC -3'
(R):5'- TGCAATCTTGGGGAGTCAC -3'

Posted On

2014-03-14