Mutagenetix > Incidental Mutation

Incidental Mutation 'R9483:Ddx39a'

716379

Institutional Source

Beutler Lab

Gene Symbol

Ddx39a

Ensembl Gene

ENSMUSG00000005481

Gene Name

DEAD box helicase 39a

Synonyms

BAT1, 2610307C23Rik, Ddx39

MMRRC Submission

Accession Numbers

Essential gene?

Probably essential (E-score: 0.940) question?

Stock #

R9483 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

84441806-84453521 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 84448916 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 264 (Y264H)

Ref Sequence

ENSEMBL: ENSMUSP00000019576 (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

probably benign
Transcript: ENSMUST00000019576
AA Change: Y264H

PolyPhen 2 Score 0.140 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000019576
Gene: ENSMUSG00000005481
AA Change: Y264H

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

probably benign
Transcript: ENSMUST00000109810
AA Change: Y264H

PolyPhen 2 Score 0.140 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000105435
Gene: ENSMUSG00000005481
AA Change: Y264H

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: 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

Predicted Effect

probably benign
Transcript: ENSMUST00000172396
AA Change: Y264H

PolyPhen 2 Score 0.140 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000132222
Gene: ENSMUSG00000005481
AA Change: Y264H

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: ENSMUST00000212949
AA Change: Y264H

PolyPhen 2 Score 0.140 (Sensitivity: 0.92; Specificity: 0.86)

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.2%

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2900026A02Rik	A	T	5: 113,339,010 (GRCm39)	M334K	probably benign	Het
Abca1	A	T	4: 53,060,351 (GRCm39)	I1525N	probably benign	Het
Abca4	A	T	3: 121,879,275 (GRCm39)	I398F		Het
Acbd3	A	G	1: 180,572,721 (GRCm39)	D327G	probably benign	Het
Acsm3	A	G	7: 119,383,166 (GRCm39)	T544A	probably damaging	Het
Atp11a	C	T	8: 12,901,087 (GRCm39)	T972M	probably damaging	Het
Cbfb	C	T	8: 105,929,123 (GRCm39)	R147*	probably null	Het
Ccdc17	G	T	4: 116,454,144 (GRCm39)	R54L	probably benign	Het
Cracdl	T	G	1: 37,670,496 (GRCm39)	E148A	probably damaging	Het
Cuedc2	G	T	19: 46,319,399 (GRCm39)	A223E	probably benign	Het
Cul5	T	C	9: 53,532,474 (GRCm39)	I787V	probably benign	Het
D430041D05Rik	T	A	2: 104,087,563 (GRCm39)	H471L	probably benign	Het
Dlgap3	C	A	4: 127,127,665 (GRCm39)	R778S	probably damaging	Het
Esrrg	T	C	1: 187,930,848 (GRCm39)	V313A	probably damaging	Het
Fam124a	T	C	14: 62,844,100 (GRCm39)	I536T	probably damaging	Het
Fbxo21	T	C	5: 118,127,272 (GRCm39)	F275L	possibly damaging	Het
Gabrg1	C	A	5: 70,999,558 (GRCm39)	G2V	possibly damaging	Het
Gcc1	G	T	6: 28,418,089 (GRCm39)	A748D	probably damaging	Het
Gjb6	T	C	14: 57,361,511 (GRCm39)	D250G	probably benign	Het
Gm44501	A	T	17: 40,889,872 (GRCm39)	K129*	probably null	Het
Hmcn2	T	G	2: 31,320,375 (GRCm39)	L3952R		Het
Hpd	A	G	5: 123,312,535 (GRCm39)	I278T	probably damaging	Het
Igsf3	T	A	3: 101,346,904 (GRCm39)	F613Y	probably damaging	Het
Igsf3	T	C	3: 101,346,817 (GRCm39)	F584S	probably damaging	Het
Ik	A	G	18: 36,886,635 (GRCm39)	D369G	probably benign	Het
Ikbke	A	G	1: 131,198,719 (GRCm39)	L365P	probably damaging	Het
Il22ra2	A	T	10: 19,508,542 (GRCm39)	Q190L	possibly damaging	Het
Itga6	T	C	2: 71,679,834 (GRCm39)	V1033A	probably benign	Het
Kif18a	T	C	2: 109,120,032 (GRCm39)	Y112H	probably damaging	Het
Krt75	T	C	15: 101,482,238 (GRCm39)	H10R	probably benign	Het
L3mbtl1	T	A	2: 162,790,734 (GRCm39)	L93H	probably benign	Het
Lrfn1	G	A	7: 28,158,183 (GRCm39)	C34Y	probably damaging	Het
Lrrc47	A	T	4: 154,101,920 (GRCm39)	I396F	probably damaging	Het
Mgat3	T	A	15: 80,095,641 (GRCm39)	V156E	probably benign	Het
Mtus2	A	G	5: 148,232,300 (GRCm39)	D1120G	possibly damaging	Het
Muc5ac	G	T	7: 141,365,465 (GRCm39)	E2700*	probably null	Het
Nxpe5	A	T	5: 138,228,591 (GRCm39)		probably benign	Het
Or51v15-ps1	T	C	7: 103,278,931 (GRCm39)	T79A	probably damaging	Het
Or5aq6	A	T	2: 86,923,390 (GRCm39)	M117K	possibly damaging	Het
Pcdhga4	T	A	18: 37,819,746 (GRCm39)	S432T	possibly damaging	Het
Pdk4	T	A	6: 5,486,716 (GRCm39)	M353L	probably benign	Het
Ppp1r13b	T	A	12: 111,800,210 (GRCm39)	K645N	probably benign	Het
Ppt1	A	T	4: 122,751,367 (GRCm39)	D288V	possibly damaging	Het
Prkcb	A	G	7: 122,181,663 (GRCm39)	Y417C	probably damaging	Het
Prss22	A	G	17: 24,215,721 (GRCm39)	I67T	probably damaging	Het
Rab29	T	C	1: 131,795,508 (GRCm39)	V40A	possibly damaging	Het
Rae1	T	C	2: 172,849,941 (GRCm39)		probably null	Het
Rasa3	C	T	8: 13,630,033 (GRCm39)		probably null	Het
Rasgrp3	A	G	17: 75,807,717 (GRCm39)	D258G	probably benign	Het
Rcc1	T	A	4: 132,062,808 (GRCm39)	T208S	probably benign	Het
Rgs3	C	A	4: 62,575,354 (GRCm39)	Y580*	probably null	Het
Rpe65	C	T	3: 159,328,318 (GRCm39)	P405S	probably damaging	Het
Rsf1	GGCGGC	GGCGGCGGCAGCGGC	7: 97,229,137 (GRCm39)		probably benign	Het
Rsph4a	A	G	10: 33,790,418 (GRCm39)	E669G	probably damaging	Het
Rusc1	A	T	3: 88,994,113 (GRCm39)	V964E	probably benign	Het
Rusc2	A	G	4: 43,415,897 (GRCm39)	N401S	probably damaging	Het
Slc10a1	G	T	12: 81,002,864 (GRCm39)	T258K	probably damaging	Het
Slc5a9	A	G	4: 111,747,418 (GRCm39)	L323P	probably damaging	Het
Slc6a17	T	A	3: 107,378,772 (GRCm39)	I637F	possibly damaging	Het
Slc8a2	A	G	7: 15,886,780 (GRCm39)	E641G	possibly damaging	Het
Sptbn2	G	T	19: 4,789,974 (GRCm39)	A1321S	probably damaging	Het
Ssh2	G	T	11: 77,283,976 (GRCm39)	A77S	possibly damaging	Het
St13	G	T	15: 81,250,587 (GRCm39)	N316K	probably damaging	Het
Taf10	A	G	7: 105,393,062 (GRCm39)	M121T	probably benign	Het
Tcta	T	C	9: 108,182,942 (GRCm39)	T68A	probably damaging	Het
Timd2	A	T	11: 46,577,889 (GRCm39)	Y81N	probably damaging	Het
Tln2	T	C	9: 67,299,769 (GRCm39)	E161G	probably damaging	Het
Tmed10	T	C	12: 85,397,621 (GRCm39)	I123V	probably benign	Het
Ttf1	T	C	2: 28,969,492 (GRCm39)		probably null	Het
Tubg1	A	G	11: 101,016,886 (GRCm39)	D396G	probably damaging	Het
Uhmk1	A	G	1: 170,034,913 (GRCm39)		probably null	Het
Unc13a	C	T	8: 72,103,221 (GRCm39)	A922T	probably benign	Het
Usp24	T	A	4: 106,219,379 (GRCm39)	V525E	probably damaging	Het
Usp28	C	A	9: 48,947,037 (GRCm39)	Q823K	probably damaging	Het
Vldlr	A	T	19: 27,224,031 (GRCm39)	I764F	probably benign	Het
Vmn2r88	T	C	14: 51,648,641 (GRCm39)	Y62H		Het
Zfp423	T	A	8: 88,507,725 (GRCm39)	N873I	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
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
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
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'- ACATCCGGCTTTTGGGAGAG -3'
(R):5'- TTGCACAGACTTGACAAAGATCAC -3'

Sequencing Primer
(F):5'- ACTGAGGTTGGGTGCAAC -3'
(R):5'- CCACCTGAAGAAGAAGGGTGTTTAG -3'

Posted On

2022-07-18