Mutagenetix > Incidental Mutation

Incidental Mutation 'R4691:Pdgfd'

354921

Institutional Source

Beutler Lab

Gene Symbol

Pdgfd

Ensembl Gene

ENSMUSG00000032006

Gene Name

platelet-derived growth factor, D polypeptide

Synonyms

1110003I09Rik

MMRRC Submission

041942-MU

Accession Numbers

Essential gene?

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

Stock #

R4691 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

6168584-6378850 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 6288556 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Leucine at position 70 (P70L)

Ref Sequence

ENSEMBL: ENSMUSP00000149162 (fasta)

Gene Model

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

AlphaFold

Q925I7

Predicted Effect

probably damaging
Transcript: ENSMUST00000058692
AA Change: P64L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000056240
Gene: ENSMUSG00000032006
AA Change: P64L

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 damaging
Transcript: ENSMUST00000168039
AA Change: P70L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000128388
Gene: ENSMUSG00000032006
AA Change: P70L

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 damaging
Transcript: ENSMUST00000214892
AA Change: P70L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

Meta Mutation Damage Score

0.9413

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 95.0%

Validation Efficiency

97% (70/72)

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	A	T	11: 9,384,195 (GRCm39)	R3882S	probably damaging	Het
Adamts2	G	T	11: 50,647,523 (GRCm39)	V299F	probably damaging	Het
Ankrd50	A	G	3: 38,537,159 (GRCm39)	S65P	probably benign	Het
Ap4e1	T	C	2: 126,903,791 (GRCm39)	C898R	probably benign	Het
Arel1	A	T	12: 84,977,023 (GRCm39)		probably null	Het
Bag6	T	A	17: 35,358,224 (GRCm39)	V164D	probably damaging	Het
C2cd5	A	G	6: 142,975,874 (GRCm39)	S769P	possibly damaging	Het
Cables1	C	T	18: 11,973,580 (GRCm39)	Q240*	probably null	Het
Ccnb1-ps	T	A	7: 41,755,516 (GRCm39)		noncoding transcript	Het
Ccz1	A	T	5: 143,928,380 (GRCm39)	I390N	possibly damaging	Het
Ceacam23	T	A	7: 17,642,891 (GRCm39)	S434T	possibly damaging	Het
Ces1a	T	C	8: 93,759,287 (GRCm39)	H283R	probably benign	Het
Clca3b	G	A	3: 144,544,853 (GRCm39)	T378I	probably benign	Het
Cpne2	A	T	8: 95,284,849 (GRCm39)	I342F	probably damaging	Het
Cyp2d9	A	G	15: 82,340,033 (GRCm39)	D141G	probably damaging	Het
Ddias	T	A	7: 92,508,024 (GRCm39)	K630N	probably damaging	Het
Dennd4b	A	G	3: 90,179,619 (GRCm39)	T626A	probably damaging	Het
Disc1	T	C	8: 125,875,186 (GRCm39)	V554A	possibly damaging	Het
Dnah10	A	G	5: 124,852,581 (GRCm39)	T1880A	probably damaging	Het
Dnase1l1	C	T	X: 73,320,644 (GRCm39)		probably null	Het
Epop	C	T	11: 97,519,719 (GRCm39)	G130D	possibly damaging	Het
Erap1	T	C	13: 74,821,811 (GRCm39)	L722P	probably damaging	Het
Eya4	T	A	10: 23,015,966 (GRCm39)	T334S	probably benign	Het
Ezr	T	C	17: 7,026,961 (GRCm39)	I5V	probably benign	Het
Fam53c	A	C	18: 34,901,743 (GRCm39)	E220A	probably damaging	Het
Galnt12	T	C	4: 47,104,143 (GRCm39)	S134P	probably damaging	Het
Gcfc2	T	A	6: 81,918,408 (GRCm39)	L366*	probably null	Het
Gins4	T	A	8: 23,727,075 (GRCm39)	D6V	probably benign	Het
Grid1	A	G	14: 35,291,514 (GRCm39)	H807R	probably benign	Het
H2-T22	GTTTT	GTTT	17: 36,352,462 (GRCm39)		probably null	Het
Ighv1-66	T	C	12: 115,556,929 (GRCm39)	Y51C	probably benign	Het
Inpp4b	A	T	8: 82,849,282 (GRCm39)	Y901F	probably damaging	Het
Irf2	T	A	8: 47,299,222 (GRCm39)	S339T	probably damaging	Het
Itgae	G	T	11: 73,010,345 (GRCm39)	G612*	probably null	Het
Kdr	T	C	5: 76,105,259 (GRCm39)	K1037R	possibly damaging	Het
Mro	A	T	18: 74,006,397 (GRCm39)	M115L	probably benign	Het
Myo5a	A	G	9: 75,087,438 (GRCm39)	E1098G	probably damaging	Het
Nkx2-1	T	A	12: 56,580,350 (GRCm39)	M197L	probably benign	Het
Or7e165	T	C	9: 19,694,678 (GRCm39)	I83T	probably benign	Het
Pank2	T	A	2: 131,138,201 (GRCm39)	F430L	possibly damaging	Het
Pcx	T	A	19: 4,669,505 (GRCm39)	V794E	probably damaging	Het
Pla2g4e	T	C	2: 120,004,781 (GRCm39)	Y521C	probably damaging	Het
Pou5f1	T	A	17: 35,817,028 (GRCm39)	F11Y	probably damaging	Het
Prdm9	A	G	17: 15,773,640 (GRCm39)	M252T	probably benign	Het
Ptk2b	C	T	14: 66,394,518 (GRCm39)	G859S	probably benign	Het
Rad51ap1	A	G	6: 126,904,516 (GRCm39)	S123P	probably benign	Het
Robo3	T	C	9: 37,336,514 (GRCm39)	E418G	probably damaging	Het
Sos2	C	T	12: 69,663,102 (GRCm39)	R631H	probably damaging	Het
Sp140l1	C	T	1: 85,066,521 (GRCm39)		probably benign	Het
St3gal2	C	T	8: 111,684,417 (GRCm39)	T25I	probably benign	Het
Stra6l	G	A	4: 45,882,851 (GRCm39)	A521T	probably benign	Het
Syt7	T	A	19: 10,403,845 (GRCm39)	L177Q	probably damaging	Het
Tet2	T	A	3: 133,191,844 (GRCm39)	Q863H	possibly damaging	Het
Tmem232	T	C	17: 65,572,237 (GRCm39)	K585E	possibly damaging	Het
Trpc6	A	C	9: 8,652,979 (GRCm39)	E595A	probably damaging	Het
Txnl1	A	G	18: 63,804,750 (GRCm39)	V248A	possibly damaging	Het
Vmn2r72	A	T	7: 85,387,119 (GRCm39)	L815*	probably null	Het
Vmn2r81	C	T	10: 79,129,211 (GRCm39)	Q701*	probably null	Het
Vps13c	T	C	9: 67,860,217 (GRCm39)	V2811A	possibly damaging	Het
Vsig10l2	T	C	9: 35,428,158 (GRCm39)	S106G	possibly damaging	Het
Zfp354a	A	G	11: 50,961,064 (GRCm39)	E425G	probably damaging	Het
Zfp617	A	T	8: 72,686,659 (GRCm39)	T330S	probably benign	Het
Zfp663	G	T	2: 165,201,050 (GRCm39)		probably benign	Het
Zfp84	T	C	7: 29,476,505 (GRCm39)	L399P	probably damaging	Het
Zfp869	A	T	8: 70,159,513 (GRCm39)	C353*	probably null	Het
Zscan22	C	T	7: 12,640,488 (GRCm39)	A85V	probably benign	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
R1563:Pdgfd	UTSW	9	6,293,939 (GRCm39)	critical splice donor site	probably null
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
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'- AGAAGTACTTTGAAATGTCATGTTGT -3'
(R):5'- TTGGGTAATTCCAAAGAGTTTAAGAA -3'

Sequencing Primer
(F):5'- ACCTCACAGACTTGTACC -3'
(R):5'- TCCATGTTTTTAATTCACATTTTCCC -3'

Posted On

2015-10-21