Mutagenetix > Incidental Mutation

Incidental Mutation 'R1563:Pdgfd'

170759

Institutional Source

Beutler Lab

Gene Symbol

Pdgfd

Ensembl Gene

ENSMUSG00000032006

Gene Name

platelet-derived growth factor, D polypeptide

Synonyms

1110003I09Rik

MMRRC Submission

039602-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.085) question?

Stock #

R1563 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

6168584-6378850 bp(+) (GRCm39)

Type of Mutation

critical splice donor site (2 bp from exon)

DNA Base Change (assembly)

T to C at 6293939 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000149162 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000058692] [ENSMUST00000168039] [ENSMUST00000214892]

AlphaFold

Q925I7

Predicted Effect

probably null
Transcript: ENSMUST00000058692

SMART Domains

Protein: ENSMUSP00000056240
Gene: ENSMUSG00000032006

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
CUB	48	164	5.38e-25	SMART
PDGF	265	358	4.58e-3	SMART

Predicted Effect

probably null
Transcript: ENSMUST00000168039

SMART Domains

Protein: ENSMUSP00000128388
Gene: ENSMUSG00000032006

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
CUB	54	170	5.38e-25	SMART
PDGF	271	364	4.58e-3	SMART

Predicted Effect

probably null
Transcript: ENSMUST00000214892

Meta Mutation Damage Score

0.9489

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.2%
20x: 92.4%

Validation Efficiency

98% (82/84)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the platelet-derived growth factor family. The four members of this family are mitogenic factors for cells of mesenchymal origin and are characterized by a core motif of eight cysteines, seven of which are found in this factor. This gene product only forms homodimers and, therefore, does not dimerize with the other three family members. It differs from alpha and beta members of this family in having an unusual N-terminal domain, the CUB domain. Two splice variants have been identified for this gene. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930519G04Rik	T	C	5: 115,001,569 (GRCm39)	M22T	probably benign	Het
A930018M24Rik	A	G	14: 51,134,576 (GRCm39)	L22P	probably damaging	Het
Aipl1	A	T	11: 71,927,538 (GRCm39)	M59K	probably damaging	Het
Atg2b	T	C	12: 105,589,747 (GRCm39)	I1835V	probably damaging	Het
Cacna1i	A	T	15: 80,274,056 (GRCm39)		probably benign	Het
Cacna1i	T	C	15: 80,205,389 (GRCm39)	V115A	probably damaging	Het
Catsperb	T	A	12: 101,554,361 (GRCm39)	M685K	probably damaging	Het
Cdh10	T	A	15: 18,986,853 (GRCm39)	Y361*	probably null	Het
Clcn4	C	T	7: 7,296,981 (GRCm39)	C219Y	probably damaging	Het
Cpeb2	G	A	5: 43,443,080 (GRCm39)	V924M	probably damaging	Het
Cpxm2	T	C	7: 131,745,411 (GRCm39)	E138G	probably benign	Het
Dennd1a	T	C	2: 37,748,441 (GRCm39)	Y346C	probably damaging	Het
Dnah8	T	A	17: 30,854,638 (GRCm39)	L100Q	probably benign	Het
Dnajc6	A	C	4: 101,456,334 (GRCm39)	N76T	probably damaging	Het
Ehbp1	A	G	11: 22,009,231 (GRCm39)	L954P	probably damaging	Het
Eral1	A	T	11: 77,966,232 (GRCm39)	D315E	probably benign	Het
Fbln2	G	T	6: 91,240,365 (GRCm39)	E724*	probably null	Het
Fyco1	A	G	9: 123,656,247 (GRCm39)		probably benign	Het
Fzd3	T	A	14: 65,473,173 (GRCm39)	E198D	probably damaging	Het
Fzd9	T	C	5: 135,279,408 (GRCm39)	N159S	probably damaging	Het
Galnt6	T	A	15: 100,601,259 (GRCm39)	Q340L	probably benign	Het
Gm20939	C	T	17: 95,184,522 (GRCm39)	A390V	probably damaging	Het
Gm5435	T	G	12: 82,542,464 (GRCm39)		noncoding transcript	Het
Gm9949	A	C	18: 62,317,089 (GRCm39)		probably benign	Het
Gprc5b	G	A	7: 118,582,984 (GRCm39)	T295I	probably benign	Het
Gria2	G	T	3: 80,598,704 (GRCm39)	Q777K	probably damaging	Het
Gtf3c3	C	T	1: 54,456,937 (GRCm39)	A488T	probably damaging	Het
Haao	T	C	17: 84,142,318 (GRCm39)	T174A	probably benign	Het
Hes6	A	T	1: 91,340,858 (GRCm39)	M1K	probably null	Het
Hook3	G	T	8: 26,600,780 (GRCm39)	Q43K	probably benign	Het
Klhl35	T	C	7: 99,120,902 (GRCm39)	V390A	probably damaging	Het
Myh9	G	T	15: 77,656,057 (GRCm39)	T1151K	probably damaging	Het
Nbn	A	T	4: 15,981,668 (GRCm39)	I587F	possibly damaging	Het
Nek4	A	G	14: 30,704,408 (GRCm39)	D696G	probably damaging	Het
Niban1	A	T	1: 151,591,424 (GRCm39)	Y522F	possibly damaging	Het
Nlrp2	T	C	7: 5,311,724 (GRCm39)	D52G	probably damaging	Het
Oit3	G	T	10: 59,263,896 (GRCm39)	R413S	probably damaging	Het
Or4k48	T	A	2: 111,476,027 (GRCm39)	H105L	probably damaging	Het
Or6c1b	A	G	10: 129,273,580 (GRCm39)	M300V	probably benign	Het
Otof	T	C	5: 30,528,349 (GRCm39)	T1870A	probably benign	Het
Pitrm1	T	C	13: 6,613,506 (GRCm39)	V526A	possibly damaging	Het
Pknox1	T	C	17: 31,814,256 (GRCm39)	S194P	probably damaging	Het
Plekhg5	T	C	4: 152,181,266 (GRCm39)	S8P	probably benign	Het
Ppp1r13b	T	C	12: 111,807,416 (GRCm39)	E157G	probably damaging	Het
Psmd3	C	T	11: 98,585,051 (GRCm39)	R466W	probably damaging	Het
Ptgfrn	A	G	3: 100,967,967 (GRCm39)	F542S	possibly damaging	Het
Ptgs1	A	T	2: 36,135,214 (GRCm39)	M393L	possibly damaging	Het
Qpct	T	A	17: 79,371,492 (GRCm39)	S87T	probably benign	Het
Qtrt1	T	A	9: 21,330,607 (GRCm39)	V269D	probably benign	Het
Rassf9	C	G	10: 102,380,821 (GRCm39)	R68G	probably damaging	Het
Relch	A	G	1: 105,647,259 (GRCm39)	Y707C	probably damaging	Het
Rif1	A	G	2: 51,963,235 (GRCm39)	E25G	probably damaging	Het
Rnf213	T	C	11: 119,305,352 (GRCm39)	F528L	probably benign	Het
Sgip1	T	C	4: 102,823,457 (GRCm39)	S693P	probably benign	Het
She	A	G	3: 89,761,921 (GRCm39)	D460G	probably benign	Het
Sipa1l1	G	T	12: 82,387,935 (GRCm39)	V54L	probably benign	Het
Slc8a3	T	A	12: 81,251,781 (GRCm39)	D640V	possibly damaging	Het
Smurf1	T	A	5: 144,819,323 (GRCm39)	E601D	probably damaging	Het
Sned1	G	A	1: 93,209,376 (GRCm39)	V830M	possibly damaging	Het
Synpo2l	A	G	14: 20,711,346 (GRCm39)	S425P	probably damaging	Het
Tbck	T	C	3: 132,421,454 (GRCm39)	V187A	possibly damaging	Het
Tcf23	A	T	5: 31,126,175 (GRCm39)	H18L	probably benign	Het
Tcp11l2	A	G	10: 84,420,808 (GRCm39)	S16G	probably damaging	Het
Tekt2	T	A	4: 126,217,200 (GRCm39)	M233L	probably benign	Het
Tex14	T	C	11: 87,427,634 (GRCm39)	S29P	probably damaging	Het
Tjp2	T	A	19: 24,110,067 (GRCm39)	N59I	probably damaging	Het
Tlr5	G	A	1: 182,802,575 (GRCm39)	M626I	probably benign	Het
Tnn	A	T	1: 159,952,985 (GRCm39)	V685D	probably damaging	Het
Trappc9	G	A	15: 72,897,816 (GRCm39)	R377W	probably damaging	Het
Trhr	G	A	15: 44,060,497 (GRCm39)	V6I	probably benign	Het
Trim30c	C	T	7: 104,032,158 (GRCm39)	R301Q	probably benign	Het
Usp51	T	C	X: 151,790,988 (GRCm39)	I194T	probably benign	Het
Vmn2r63	A	G	7: 42,553,550 (GRCm39)	S569P	probably benign	Het
Vps26a	T	G	10: 62,300,459 (GRCm39)	I236L	probably benign	Het
Zc3h7b	C	T	15: 81,661,289 (GRCm39)	P376L	probably benign	Het
Zcchc14	T	C	8: 122,330,718 (GRCm39)	M882V	probably benign	Het
Zfhx2	A	G	14: 55,302,545 (GRCm39)	V1813A	probably benign	Het
Zswim2	C	T	2: 83,745,626 (GRCm39)	G604D	possibly damaging	Het
Zzef1	C	T	11: 72,739,559 (GRCm39)	Q669*	probably null	Het

Other mutations in Pdgfd

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00545:Pdgfd	APN	9	6,288,621 (GRCm39)	nonsense	probably null
IGL00806:Pdgfd	APN	9	6,288,667 (GRCm39)	missense	probably benign	0.00
IGL01481:Pdgfd	APN	9	6,337,271 (GRCm39)	missense	probably null	0.62
IGL01704:Pdgfd	APN	9	6,337,327 (GRCm39)	missense	probably damaging	1.00
IGL02951:Pdgfd	APN	9	6,288,494 (GRCm39)	missense	probably damaging	1.00
IGL03022:Pdgfd	APN	9	6,288,495 (GRCm39)	missense	probably damaging	1.00
R0122:Pdgfd	UTSW	9	6,293,851 (GRCm39)	missense	probably damaging	1.00
R0408:Pdgfd	UTSW	9	6,293,928 (GRCm39)	nonsense	probably null
R0542:Pdgfd	UTSW	9	6,359,769 (GRCm39)	missense	probably damaging	1.00
R0701:Pdgfd	UTSW	9	6,359,706 (GRCm39)	missense	probably damaging	0.98
R1376:Pdgfd	UTSW	9	6,376,994 (GRCm39)	missense	probably benign	0.00
R1376:Pdgfd	UTSW	9	6,376,994 (GRCm39)	missense	probably benign	0.00
R2513:Pdgfd	UTSW	9	6,359,894 (GRCm39)	missense	probably damaging	1.00
R3751:Pdgfd	UTSW	9	6,337,447 (GRCm39)	splice site	probably benign
R3831:Pdgfd	UTSW	9	6,359,762 (GRCm39)	missense	probably damaging	1.00
R3832:Pdgfd	UTSW	9	6,359,762 (GRCm39)	missense	probably damaging	1.00
R3833:Pdgfd	UTSW	9	6,359,762 (GRCm39)	missense	probably damaging	1.00
R4691:Pdgfd	UTSW	9	6,288,556 (GRCm39)	missense	probably damaging	1.00
R6280:Pdgfd	UTSW	9	6,288,627 (GRCm39)	missense	probably benign	0.00
R6622:Pdgfd	UTSW	9	6,293,818 (GRCm39)	missense	probably damaging	1.00
R7488:Pdgfd	UTSW	9	6,359,739 (GRCm39)	missense	probably damaging	1.00
R7581:Pdgfd	UTSW	9	6,293,894 (GRCm39)	missense	probably damaging	1.00
R7873:Pdgfd	UTSW	9	6,337,271 (GRCm39)	missense	probably benign	0.06
R7883:Pdgfd	UTSW	9	6,293,939 (GRCm39)	critical splice donor site	probably null
R8498:Pdgfd	UTSW	9	6,288,655 (GRCm39)	missense	probably damaging	1.00
R8788:Pdgfd	UTSW	9	6,377,000 (GRCm39)	missense	probably benign	0.00
R9147:Pdgfd	UTSW	9	6,333,328 (GRCm39)	missense	probably benign	0.09
R9148:Pdgfd	UTSW	9	6,333,328 (GRCm39)	missense	probably benign	0.09
R9386:Pdgfd	UTSW	9	6,293,903 (GRCm39)	missense	possibly damaging	0.81
R9747:Pdgfd	UTSW	9	6,337,310 (GRCm39)	missense	probably benign	0.09
RF009:Pdgfd	UTSW	9	6,288,624 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CAGCACTGTTGTCAGAGGAAGATGG -3'
(R):5'- CAGTCTCTTGGTCAGCAACATGGG -3'

Sequencing Primer
(F):5'- TCAGAGGAAGATGGTGTGGC -3'
(R):5'- cactaccaccaccaccac -3'

Posted On

2014-04-13