Mutagenetix > Incidental Mutation

Incidental Mutation 'R0542:Pdgfd'

49986

Institutional Source

Beutler Lab

Gene Symbol

Pdgfd

Ensembl Gene

ENSMUSG00000032006

Gene Name

platelet-derived growth factor, D polypeptide

Synonyms

1110003I09Rik

MMRRC Submission

038734-MU

Accession Numbers

Essential gene?

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

Stock #

R0542 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

6168584-6378850 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 6359769 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 280 (N280S)

Ref Sequence

ENSEMBL: ENSMUSP00000128388 (fasta)

Gene Model

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

AlphaFold

Q925I7

Predicted Effect

probably damaging
Transcript: ENSMUST00000058692
AA Change: N274S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000056240
Gene: ENSMUSG00000032006
AA Change: N274S

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: N280S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000128388
Gene: ENSMUSG00000032006
AA Change: N280S

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 benign
Transcript: ENSMUST00000214892

Meta Mutation Damage Score

0.3405

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.1%
20x: 95.0%

Validation Efficiency

99% (70/71)

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abhd12b	C	A	12: 70,210,269 (GRCm39)	N71K	possibly damaging	Het
Adgrl2	A	G	3: 148,564,854 (GRCm39)	I242T	probably damaging	Het
Adgrv1	A	G	13: 81,721,437 (GRCm39)	S714P	probably damaging	Het
Agap3	G	A	5: 24,705,184 (GRCm39)	R704Q	possibly damaging	Het
Ankrd11	T	C	8: 123,622,509 (GRCm39)	R448G	probably damaging	Het
Anks1b	T	C	10: 89,909,829 (GRCm39)		probably benign	Het
Caml	A	T	13: 55,770,974 (GRCm39)	Q24L	possibly damaging	Het
Cdc14b	G	A	13: 64,391,497 (GRCm39)	T124I	probably benign	Het
Clca3a2	A	G	3: 144,781,571 (GRCm39)		probably benign	Het
Col12a1	A	G	9: 79,512,610 (GRCm39)		probably null	Het
Crispld1	T	C	1: 17,816,992 (GRCm39)	V183A	possibly damaging	Het
Cstdc1	A	G	2: 148,624,092 (GRCm39)	N22S	probably benign	Het
Dhx40	C	T	11: 86,695,082 (GRCm39)		probably null	Het
Dmxl1	T	A	18: 50,026,761 (GRCm39)	D1956E	probably benign	Het
Dsc2	A	G	18: 20,184,283 (GRCm39)	V35A	probably damaging	Het
Dync2i2	A	G	2: 29,921,837 (GRCm39)	V508A	probably damaging	Het
Elovl2	A	G	13: 41,345,452 (GRCm39)		probably benign	Het
Gapvd1	T	C	2: 34,615,048 (GRCm39)		probably benign	Het
Gnaq	T	A	19: 16,196,982 (GRCm39)	I56N	probably damaging	Het
Gpr139	T	C	7: 118,744,306 (GRCm39)	D93G	probably benign	Het
Hars1	C	T	18: 36,904,234 (GRCm39)	R215H	probably benign	Het
Helz2	C	A	2: 180,873,882 (GRCm39)	W2204L	probably damaging	Het
Ift70b	A	G	2: 75,767,055 (GRCm39)	V566A	probably damaging	Het
Itgb6	A	T	2: 60,435,480 (GRCm39)	C757S	possibly damaging	Het
Kpnb1	G	A	11: 97,078,398 (GRCm39)	T5I	probably benign	Het
Krt82	T	C	15: 101,454,035 (GRCm39)		probably benign	Het
Lgals9	T	A	11: 78,860,546 (GRCm39)	K175N	possibly damaging	Het
Lrp2	A	G	2: 69,258,998 (GRCm39)	I4564T	probably benign	Het
Mblac1	A	G	5: 138,192,798 (GRCm39)	T47A	possibly damaging	Het
Med12l	G	A	3: 58,949,822 (GRCm39)	D182N	probably damaging	Het
Megf9	A	G	4: 70,353,585 (GRCm39)	I407T	probably benign	Het
Mtmr6	A	T	14: 60,529,578 (GRCm39)		probably null	Het
Mtor	A	G	4: 148,624,907 (GRCm39)	T2173A	probably benign	Het
Mzt1	A	T	14: 99,277,938 (GRCm39)		probably benign	Het
Narf	T	C	11: 121,143,690 (GRCm39)	L444P	probably damaging	Het
Nsd1	A	T	13: 55,408,271 (GRCm39)	Q1305L	possibly damaging	Het
Ntsr1	A	G	2: 180,184,374 (GRCm39)	Y359C	probably damaging	Het
Olfm1	A	G	2: 28,104,640 (GRCm39)	D159G	possibly damaging	Het
Or2l13b	A	T	16: 19,348,732 (GRCm39)	*313R	probably null	Het
Pcdh1	C	T	18: 38,322,975 (GRCm39)	V953I	probably damaging	Het
Pcdhb11	A	T	18: 37,556,887 (GRCm39)	D739V	probably damaging	Het
Per2	A	T	1: 91,366,054 (GRCm39)		probably null	Het
Pfkp	G	T	13: 6,672,028 (GRCm39)	C122*	probably null	Het
Plxna4	G	A	6: 32,169,232 (GRCm39)	R1322W	probably damaging	Het
Ppox	A	G	1: 171,106,818 (GRCm39)	L202P	probably damaging	Het
Ppp1r3e	G	A	14: 55,114,588 (GRCm39)	P58L	probably benign	Het
Prr23a2	A	C	9: 98,739,086 (GRCm39)	N148T	probably benign	Het
Psd	T	C	19: 46,302,649 (GRCm39)	T842A	probably damaging	Het
Ranbp2	C	T	10: 58,314,236 (GRCm39)	A1652V	probably benign	Het
Rragd	G	A	4: 33,007,103 (GRCm39)	V144M	probably damaging	Het
Sema6a	T	G	18: 47,381,643 (GRCm39)	D968A	probably damaging	Het
Slc30a5	A	T	13: 100,945,793 (GRCm39)		probably null	Het
Snx17	G	T	5: 31,353,895 (GRCm39)		probably null	Het
Styxl2	A	T	1: 165,928,853 (GRCm39)	M253K	possibly damaging	Het
Syt14	G	T	1: 192,613,111 (GRCm39)	T563K	probably damaging	Het
Tada3	T	C	6: 113,352,175 (GRCm39)	K85E	probably damaging	Het
Tspear	T	C	10: 77,716,921 (GRCm39)	V532A	probably benign	Het
Ttn	A	T	2: 76,723,453 (GRCm39)	C6426S	possibly damaging	Het
Unc79	T	C	12: 103,060,437 (GRCm39)		probably benign	Het
Usp19	A	G	9: 108,371,584 (GRCm39)		probably null	Het
Vav3	G	A	3: 109,434,746 (GRCm39)	D426N	probably damaging	Het
Vezt	T	C	10: 93,842,958 (GRCm39)		probably null	Het
Vldlr	G	T	19: 27,213,655 (GRCm39)	R114L	probably benign	Het
Wwc2	C	T	8: 48,321,414 (GRCm39)	V567I	unknown	Het
Zfp423	T	C	8: 88,507,237 (GRCm39)	T911A	probably damaging	Het
Zfp719	A	G	7: 43,238,677 (GRCm39)		probably null	Het
Zkscan16	A	T	4: 58,956,597 (GRCm39)	H293L	possibly damaging	Het
Zkscan6	A	C	11: 65,719,525 (GRCm39)	N515T	possibly damaging	Het
Znfx1	A	G	2: 166,897,575 (GRCm39)	S450P	probably damaging	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
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
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'- TGCACAAGTTGTAGGGCTTGAACC -3'
(R):5'- GGCCTGACATTACTGATGCTGTACC -3'

Sequencing Primer
(F):5'- GTGTTCCATAGTAAGATCCCAGG -3'
(R):5'- ACTGATGCTGTACCTCATGATAC -3'

Posted On

2013-06-12