Mutagenetix > Incidental Mutation

Incidental Mutation 'R6280:Pdgfd'

507907

Institutional Source

Beutler Lab

Gene Symbol

Pdgfd

Ensembl Gene

ENSMUSG00000032006

Gene Name

platelet-derived growth factor, D polypeptide

Synonyms

1110003I09Rik

MMRRC Submission

044450-MU

Accession Numbers

Essential gene?

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

Stock #

R6280 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

6168584-6378850 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 6288627 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 94 (S94T)

Ref Sequence

ENSEMBL: ENSMUSP00000149162 (fasta)

Gene Model

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

AlphaFold

Q925I7

Predicted Effect

probably benign
Transcript: ENSMUST00000058692
AA Change: S88T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000056240
Gene: ENSMUSG00000032006
AA Change: S88T

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 benign
Transcript: ENSMUST00000168039
AA Change: S94T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000128388
Gene: ENSMUSG00000032006
AA Change: S94T

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
AA Change: S94T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.5%
20x: 95.9%

Validation Efficiency

100% (75/75)

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: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca12	C	T	1: 71,311,619 (GRCm39)	D1930N	probably benign	Het
Adam8	A	G	7: 139,564,720 (GRCm39)	L667S	probably damaging	Het
Adcy4	A	T	14: 56,016,500 (GRCm39)	I317N	probably damaging	Het
Agpat3	A	G	10: 78,120,872 (GRCm39)	F102S	probably damaging	Het
Apbb2	A	T	5: 66,522,325 (GRCm39)	W443R	probably damaging	Het
BC049715	T	A	6: 136,817,229 (GRCm39)	Y156*	probably null	Het
Bpifc	C	T	10: 85,813,576 (GRCm39)	V323I	probably benign	Het
Camp	T	G	9: 109,676,577 (GRCm39)	I149L	probably benign	Het
Cfap20dc	T	G	14: 8,473,414 (GRCm38)		probably null	Het
Cibar2	A	G	8: 120,898,858 (GRCm39)	I94T	possibly damaging	Het
Cnih1	A	G	14: 47,025,634 (GRCm39)		probably null	Het
Col18a1	A	T	10: 76,948,323 (GRCm39)		probably benign	Het
Dsg4	A	T	18: 20,599,724 (GRCm39)	D780V	probably damaging	Het
Dync1i1	G	A	6: 5,972,084 (GRCm39)	V442I	probably benign	Het
Fam83g	G	T	11: 61,594,008 (GRCm39)	S514I	probably benign	Het
Fbxo7	A	G	10: 85,864,969 (GRCm39)	N93D	probably benign	Het
Fgf20	G	T	8: 40,734,153 (GRCm39)	S76*	probably null	Het
Foxi1	A	G	11: 34,157,972 (GRCm39)	F18L	probably damaging	Het
Fxr1	G	A	3: 34,100,401 (GRCm39)		probably benign	Het
Gon4l	T	A	3: 88,798,195 (GRCm39)	L800H	probably damaging	Het
Gpn3	T	A	5: 122,512,022 (GRCm39)	S33T	probably benign	Het
Gria4	T	C	9: 4,456,072 (GRCm39)	M743V	probably damaging	Het
Hira	A	G	16: 18,729,457 (GRCm39)	N109D	probably damaging	Het
Hsd3b3	A	G	3: 98,660,621 (GRCm39)		probably null	Het
Hsf2	T	G	10: 57,387,591 (GRCm39)	S370A	probably benign	Het
Htt	T	A	5: 35,028,103 (GRCm39)	D1786E	probably benign	Het
Ifit1bl2	T	A	19: 34,597,534 (GRCm39)	R27S	possibly damaging	Het
Il17rb	G	A	14: 29,724,928 (GRCm39)	A186V	probably benign	Het
Irak4	G	T	15: 94,449,691 (GRCm39)	E57*	probably null	Het
Kcnh2	T	A	5: 24,536,921 (GRCm39)	H221L	probably benign	Het
Kdm2b	T	C	5: 123,016,687 (GRCm39)	N1149D	probably damaging	Het
Kif26a	A	G	12: 112,141,303 (GRCm39)	H702R	probably damaging	Het
Kmt2e	T	C	5: 23,704,514 (GRCm39)	S1236P	possibly damaging	Het
Krt77	T	A	15: 101,773,910 (GRCm39)	D248V	probably damaging	Het
Lgals3bp	T	C	11: 118,284,106 (GRCm39)	N52S	possibly damaging	Het
Lhfpl6	T	C	3: 53,167,935 (GRCm39)	Y170H	probably damaging	Het
Lpin2	A	G	17: 71,539,243 (GRCm39)		probably benign	Het
Lrig3	T	C	10: 125,846,848 (GRCm39)	I872T	probably benign	Het
Lrit3	T	C	3: 129,582,412 (GRCm39)	E525G	probably damaging	Het
Lrp1	T	C	10: 127,425,453 (GRCm39)	T726A	probably benign	Het
Mep1a	A	T	17: 43,813,283 (GRCm39)	N46K	probably damaging	Het
Muc16	C	A	9: 18,490,613 (GRCm39)		probably null	Het
N4bp1	A	C	8: 87,579,794 (GRCm39)	N669K	possibly damaging	Het
Nelfcd	A	G	2: 174,257,739 (GRCm39)	D26G	probably benign	Het
Neu4	G	A	1: 93,952,873 (GRCm39)	S414N	probably damaging	Het
Nudt9	A	G	5: 104,212,935 (GRCm39)	D336G	probably benign	Het
Obscn	C	A	11: 58,954,509 (GRCm39)	G3691V	possibly damaging	Het
Or4c52	A	C	2: 89,845,393 (GRCm39)	I40L	possibly damaging	Het
Or5t17	A	G	2: 86,832,364 (GRCm39)	N17S	probably damaging	Het
Picalm	A	G	7: 89,826,770 (GRCm39)	H290R	probably benign	Het
Pou2f3	A	T	9: 43,050,634 (GRCm39)	L242Q	probably damaging	Het
Pou2f3	G	T	9: 43,050,635 (GRCm39)	L242M	probably damaging	Het
Prkd3	C	T	17: 79,289,360 (GRCm39)	G187D	probably damaging	Het
Pwp1	A	G	10: 85,710,326 (GRCm39)	S49G	probably damaging	Het
Ralgapa2	A	G	2: 146,184,129 (GRCm39)	L1626P	probably damaging	Het
Resf1	T	C	6: 149,228,555 (GRCm39)	S534P	probably damaging	Het
Rin2	A	G	2: 145,702,939 (GRCm39)	Y545C	probably damaging	Het
Rwdd4a	A	G	8: 47,995,832 (GRCm39)	T71A	probably benign	Het
Senp7	T	C	16: 55,982,738 (GRCm39)	F504L	possibly damaging	Het
Slc12a6	A	G	2: 112,167,703 (GRCm39)	T231A	probably damaging	Het
Slc13a2	CGTTATCTGT	CGT	11: 78,294,306 (GRCm39)		probably benign	Het
Slc34a1	A	G	13: 24,006,377 (GRCm39)	S468G	probably benign	Het
Slc4a10	A	G	2: 62,112,310 (GRCm39)	N697S	probably benign	Het
Spint1	T	A	2: 119,075,759 (GRCm39)	V194E	possibly damaging	Het
Sptlc2	A	T	12: 87,434,905 (GRCm39)	M14K	probably benign	Het
Stard9	A	G	2: 120,531,608 (GRCm39)	K2622E	probably benign	Het
Tbc1d5	T	C	17: 51,089,338 (GRCm39)	N614S	probably benign	Het
Tdpoz2	A	T	3: 93,559,190 (GRCm39)	C261S	probably benign	Het
Tmem150b	A	T	7: 4,727,373 (GRCm39)	I44N	probably benign	Het
Ttn	A	G	2: 76,608,502 (GRCm39)	L17807P	probably damaging	Het
Vcan	G	A	13: 89,873,492 (GRCm39)	R121W	probably damaging	Het
Vmn2r15	T	A	5: 109,441,291 (GRCm39)	H189L	possibly damaging	Het
Vmn2r19	A	G	6: 123,313,212 (GRCm39)	S761G	probably benign	Het
Wdr11	A	T	7: 129,200,830 (GRCm39)	K34*	probably null	Het
Zfp120	A	T	2: 149,959,964 (GRCm39)	S141R	possibly damaging	Het
Zfp462	C	G	4: 55,010,253 (GRCm39)	P740A	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
R4691:Pdgfd	UTSW	9	6,288,556 (GRCm39)	missense	probably damaging	1.00
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'- TGTGACTACTAACAGAGAGCAATC -3'
(R):5'- TCTGCAGTGCCAGCATAAC -3'

Sequencing Primer
(F):5'- GAGAGCAATCACCTCACAGACTTG -3'
(R):5'- GCTAGGGCCCTAAACTTCATG -3'

Posted On

2018-03-15