Mutagenetix > Incidental Mutation

Incidental Mutation 'R2935:Ddx39a'

254998

Institutional Source

Beutler Lab

Gene Symbol

Ddx39a

Ensembl Gene

ENSMUSG00000005481

Gene Name

DEAD box helicase 39a

Synonyms

BAT1, 2610307C23Rik, Ddx39

Accession Numbers

Essential gene?

Probably essential (E-score: 0.930) question?

Stock #

R2935 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

84441806-84453521 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 84447587 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Aspartic acid at position 144 (V144D)

Ref Sequence

ENSEMBL: ENSMUSP00000116101 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000002964] [ENSMUST00000019576] [ENSMUST00000075843] [ENSMUST00000109802] [ENSMUST00000109810] [ENSMUST00000172396] [ENSMUST00000140521] [ENSMUST00000212949] [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: V144D

PolyPhen 2 Score 0.514 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000019576
Gene: ENSMUSG00000005481
AA Change: V144D

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: V144D

PolyPhen 2 Score 0.514 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000105435
Gene: ENSMUSG00000005481
AA Change: V144D

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: V144D

PolyPhen 2 Score 0.514 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000132222
Gene: ENSMUSG00000005481
AA Change: V144D

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: ENSMUST00000140521
AA Change: V144D

PolyPhen 2 Score 0.574 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000116101
Gene: ENSMUSG00000005481
AA Change: V144D

Domain	Start	End	E-Value	Type
low complexity region	5	18	N/A	INTRINSIC
DEXDc	63	208	2.82e-21	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000212949
AA Change: V144D

PolyPhen 2 Score 0.514 (Sensitivity: 0.88; Specificity: 0.90)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000140606

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184114

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139797

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

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.5%

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: 22 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca17	G	C	17: 24,508,481 (GRCm39)	T1018R	probably damaging	Het
Adgrl1	T	C	8: 84,661,189 (GRCm39)	I894T	probably damaging	Het
Cd55	A	G	1: 130,380,163 (GRCm39)	S272P	possibly damaging	Het
Chek2	T	C	5: 111,015,886 (GRCm39)	V467A	probably damaging	Het
Cyp11a1	A	G	9: 57,923,673 (GRCm39)	Y126C	probably damaging	Het
Fbxl19	G	A	7: 127,351,432 (GRCm39)	R304H	probably damaging	Het
Ide	A	G	19: 37,302,706 (GRCm39)	F135L	unknown	Het
Khdc3	T	C	9: 73,010,987 (GRCm39)	V255A	possibly damaging	Het
Klk1b22	A	G	7: 43,764,146 (GRCm39)	I25V	probably benign	Het
Magi2	A	AG	5: 20,807,459 (GRCm39)		probably null	Het
Mark2	T	C	19: 7,263,254 (GRCm39)	N204S	probably benign	Het
Or1l4b	A	G	2: 37,037,123 (GRCm39)	K300E	possibly damaging	Het
Or4c123	A	T	2: 89,127,604 (GRCm39)	N3K	possibly damaging	Het
Osbpl8	T	A	10: 111,105,297 (GRCm39)	S251T	probably benign	Het
Piezo2	A	G	18: 63,279,914 (GRCm39)	I219T	probably damaging	Het
Rap1gap	T	C	4: 137,452,042 (GRCm39)	S521P	probably benign	Het
Rxrb	CGCGGCGGCGGCGGCGGCGGC	CGCGGCGGCGGCGGCGGC	17: 34,251,106 (GRCm39)		probably benign	Het
Smchd1	G	A	17: 71,718,900 (GRCm39)	P823L	probably damaging	Het
Sncaip	A	G	18: 52,971,104 (GRCm39)	D8G	probably damaging	Het
Stau1	G	A	2: 166,797,037 (GRCm39)	T120I	probably benign	Het
Stxbp5l	G	T	16: 36,954,551 (GRCm39)	H920N	possibly damaging	Het
Thsd7b	A	G	1: 129,605,824 (GRCm39)	T522A	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
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'- AGCCTGATGAATTATGCCCAAC -3'
(R):5'- ACAGGACAGTAGGATGCTCACC -3'

Sequencing Primer
(F):5'- TGATGAATTATGCCCAACCCACAAG -3'
(R):5'- GCTCACCCAGCTGTTCCAG -3'

Posted On

2014-12-29