Mutagenetix > Incidental Mutation

Incidental Mutation 'R7883:Pdgfd'

608893

Institutional Source

Beutler Lab

Gene Symbol

Pdgfd

Ensembl Gene

ENSMUSG00000032006

Gene Name

platelet-derived growth factor, D polypeptide

Synonyms

1110003I09Rik

MMRRC Submission

045935-MU

Accession Numbers

Essential gene?

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

Stock #

R7883 (G1)

Quality Score

225.009

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 A at 6293939 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000128388 (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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.2%

Validation Efficiency

99% (79/80)

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110065P20Rik	A	T	4: 124,744,440 (GRCm39)	W5R	unknown	Het
Abcb6	A	T	1: 75,154,660 (GRCm39)	S258R	possibly damaging	Het
Abcc10	A	G	17: 46,618,027 (GRCm39)	V1082A	probably benign	Het
Adrb2	A	G	18: 62,312,447 (GRCm39)	V126A	probably damaging	Het
Apol11a	A	G	15: 77,400,774 (GRCm39)	E87G	probably damaging	Het
Arhgap45	T	A	10: 79,863,423 (GRCm39)	C755*	probably null	Het
Arl13b	A	T	16: 62,647,629 (GRCm39)	I93K	probably damaging	Het
Aspm	A	G	1: 139,406,405 (GRCm39)	K1764R	possibly damaging	Het
Atp8b5	A	G	4: 43,342,471 (GRCm39)	I381V	probably damaging	Het
Atxn2	A	G	5: 121,940,180 (GRCm39)	H985R	possibly damaging	Het
Bms1	G	T	6: 118,365,735 (GRCm39)	N1150K	probably benign	Het
C1ra	G	A	6: 124,494,684 (GRCm39)	E316K	probably benign	Het
Camta2	T	C	11: 70,566,037 (GRCm39)	D749G	probably damaging	Het
Cd300ld2	CGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGTCAGAACTGTGGATGGCACAACTGTGCATGGCAGAACTGTGGATGGCACAACTGTGGATGGCAGAACTGTGG	CGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGTCAGAACTGTGGATGGCACAACTGTGCATGGCAGAACTGTGGATGGCACAACTGTGGATGGCAGAACTGTGG	11: 114,903,257 (GRCm39)		probably benign	Het
Cep152	G	A	2: 125,454,978 (GRCm39)	A274V	possibly damaging	Het
Chd7	A	G	4: 8,826,504 (GRCm39)	N956S	probably damaging	Het
Cpt1c	A	T	7: 44,613,438 (GRCm39)		probably null	Het
Cttn	C	T	7: 143,999,555 (GRCm39)	V338I	probably benign	Het
Dab2ip	G	A	2: 35,610,218 (GRCm39)	G811D	possibly damaging	Het
Dmtf1	T	C	5: 9,190,397 (GRCm39)	T106A	probably benign	Het
Dync2h1	T	C	9: 7,005,566 (GRCm39)	E3768G	possibly damaging	Het
Exoc1	T	A	5: 76,709,229 (GRCm39)	D612E	probably damaging	Het
Fat2	T	C	11: 55,144,190 (GRCm39)		probably null	Het
Fat4	G	A	3: 39,035,968 (GRCm39)	E3207K	probably damaging	Het
Fbxw18	A	G	9: 109,517,474 (GRCm39)	Y410H	probably damaging	Het
Fgfr3	T	A	5: 33,891,235 (GRCm39)	S518T	probably damaging	Het
Fzr1	G	A	10: 81,204,469 (GRCm39)	T377M	probably damaging	Het
Gcnt3	T	A	9: 69,941,453 (GRCm39)	I372F	probably damaging	Het
Gm10577	A	T	4: 100,877,719 (GRCm39)	Y59N	unknown	Het
Gm826	A	G	2: 160,169,213 (GRCm39)	L32P	unknown	Het
Grid1	T	G	14: 35,172,259 (GRCm39)		probably null	Het
Hid1	T	A	11: 115,245,435 (GRCm39)	T457S	probably damaging	Het
Hsd3b5	A	G	3: 98,529,456 (GRCm39)	V58A	probably benign	Het
Iqcj	A	G	3: 67,954,641 (GRCm39)	K49E	probably damaging	Het
Itpk1	A	G	12: 102,572,434 (GRCm39)	V93A	probably benign	Het
Kcnt2	A	G	1: 140,450,888 (GRCm39)	I722M	probably damaging	Het
Klhl36	T	C	8: 120,601,217 (GRCm39)	V412A	possibly damaging	Het
Krt18	G	A	15: 101,936,885 (GRCm39)	V58M	possibly damaging	Het
Lats2	T	C	14: 57,934,657 (GRCm39)	Y691C	probably damaging	Het
Lrp1b	A	T	2: 40,555,141 (GRCm39)	I4095N		Het
Map1a	A	G	2: 121,135,853 (GRCm39)	E2223G	probably damaging	Het
Med25	A	G	7: 44,541,232 (GRCm39)	F94L	possibly damaging	Het
Mertk	A	G	2: 128,618,265 (GRCm39)	I499V	probably benign	Het
Mrps12	A	G	7: 28,439,568 (GRCm39)	L49P	probably benign	Het
Nwd1	T	A	8: 73,393,754 (GRCm39)	V339D	probably damaging	Het
Obscn	G	A	11: 58,960,835 (GRCm39)	Q3159*	probably null	Het
Patj	G	A	4: 98,499,372 (GRCm39)	V1349I	probably benign	Het
Pcdha8	T	A	18: 37,126,196 (GRCm39)	V226D	probably damaging	Het
Pdzd7	A	C	19: 45,018,679 (GRCm39)	I600S	probably damaging	Het
Pgpep1l	G	A	7: 67,888,897 (GRCm39)	R45*	probably null	Het
Pik3c3	T	C	18: 30,407,416 (GRCm39)	S55P	probably benign	Het
Pkhd1l1	A	T	15: 44,392,522 (GRCm39)	D1619V	probably damaging	Het
Pkp1	A	G	1: 135,812,641 (GRCm39)		probably null	Het
Ppan	T	A	9: 20,802,777 (GRCm39)	I311N	probably benign	Het
Ppih	C	A	4: 119,167,987 (GRCm39)	G175W	probably damaging	Het
Ppp1r8	G	T	4: 132,562,026 (GRCm39)	Q65K	probably damaging	Het
Psmd5	T	A	2: 34,746,524 (GRCm39)	K351M	possibly damaging	Het
Pth1r	T	C	9: 110,560,626 (GRCm39)	K53R	probably benign	Het
Ptprn	A	T	1: 75,239,007 (GRCm39)	F9L	probably damaging	Het
Rgl3	T	C	9: 21,892,723 (GRCm39)	I288V	probably benign	Het
Sds	A	G	5: 120,617,278 (GRCm39)	I45V	possibly damaging	Het
Sfxn4	A	T	19: 60,847,187 (GRCm39)		probably null	Het
Sis	A	T	3: 72,828,329 (GRCm39)	C1220S	possibly damaging	Het
Slc22a16	T	G	10: 40,479,660 (GRCm39)	D577E	probably benign	Het
Slc25a10	T	A	11: 120,385,340 (GRCm39)	M43K	possibly damaging	Het
Smpd1	T	C	7: 105,206,192 (GRCm39)	I440T	probably damaging	Het
Spata6l	A	C	19: 28,906,013 (GRCm39)	S297A	probably benign	Het
St6galnac6	A	G	2: 32,504,941 (GRCm39)	N151S	probably benign	Het
Taf4	G	T	2: 179,571,088 (GRCm39)	L742M	probably damaging	Het
Tctn1	A	G	5: 122,402,375 (GRCm39)	S20P	possibly damaging	Het
Tkfc	A	T	19: 10,572,394 (GRCm39)		probably null	Het
Tmem270	A	G	5: 134,931,681 (GRCm39)	V87A	possibly damaging	Het
Tpo	T	C	12: 30,153,169 (GRCm39)	H395R	probably damaging	Het
Tufm	T	C	7: 126,088,114 (GRCm39)	F206L	possibly damaging	Het
Tulp2	A	G	7: 45,166,188 (GRCm39)		probably null	Het
Tulp3	G	A	6: 128,303,807 (GRCm39)	T264M	probably damaging	Het
Uqcrc2	A	G	7: 120,244,440 (GRCm39)	D194G	possibly damaging	Het
Vill	C	A	9: 118,894,589 (GRCm39)	C415*	probably null	Het
Zfp799	A	G	17: 33,039,256 (GRCm39)	C337R	probably damaging	Het
Zhx2	A	G	15: 57,685,270 (GRCm39)	E213G	possibly 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
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
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
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'- TCTCAGCAGCTAAAGTCAACTTTAC -3'
(R):5'- CCTTCAAATGTCATGCCCTTAAG -3'

Sequencing Primer
(F):5'- CTCACACTTTAGGTATGACTTTGTG -3'
(R):5'- CAAATGTCATGCCCTTAAGTTTGAC -3'

Posted On

2019-12-20