Mutagenetix > Incidental Mutation

Incidental Mutation 'R9475:Pdgfra'

715694

Institutional Source

Beutler Lab

Gene Symbol

Pdgfra

Ensembl Gene

ENSMUSG00000029231

Gene Name

platelet derived growth factor receptor, alpha polypeptide

Synonyms

Pdgfr-2, CD140a

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9475 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

75152292-75198215 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 75167927 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Threonine at position 240 (N240T)

Ref Sequence

ENSEMBL: ENSMUSP00000000476 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000000476] [ENSMUST00000168162] [ENSMUST00000200822] [ENSMUST00000201711] [ENSMUST00000202161] [ENSMUST00000202186] [ENSMUST00000202681] [ENSMUST00000202992]

AlphaFold

P26618

Predicted Effect

possibly damaging
Transcript: ENSMUST00000000476
AA Change: N240T

PolyPhen 2 Score 0.933 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000000476
Gene: ENSMUSG00000029231
AA Change: N240T

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
IG	34	122	6.07e-3	SMART
IG_like	135	206	1.7e1	SMART
IGc2	226	297	8.72e-4	SMART
IG	322	414	2.86e0	SMART
transmembrane domain	527	549	N/A	INTRINSIC
TyrKc	593	950	8.51e-141	SMART
Blast:TyrKc	960	991	3e-8	BLAST
low complexity region	1063	1082	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000168162
AA Change: N240T

PolyPhen 2 Score 0.933 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000127173
Gene: ENSMUSG00000029231
AA Change: N240T

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
IG	34	122	6.07e-3	SMART
IG_like	135	206	1.7e1	SMART
IGc2	226	297	8.72e-4	SMART
IG	322	414	2.86e0	SMART
transmembrane domain	527	549	N/A	INTRINSIC
TyrKc	593	950	8.51e-141	SMART
Blast:TyrKc	960	991	3e-8	BLAST
low complexity region	1063	1082	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000200822
AA Change: N240T

PolyPhen 2 Score 0.933 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000144634
Gene: ENSMUSG00000029231
AA Change: N240T

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
IG	34	122	2.6e-5	SMART
IG_like	135	206	7e-2	SMART
Blast:IG	220	243	3e-6	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000201711
AA Change: N240T

PolyPhen 2 Score 0.424 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000143891
Gene: ENSMUSG00000029231
AA Change: N240T

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
IG	34	122	6.07e-3	SMART
IG_like	135	206	1.7e1	SMART
IGc2	226	297	8.72e-4	SMART
IG	322	414	2.86e0	SMART
transmembrane domain	527	549	N/A	INTRINSIC
Pfam:Pkinase	593	701	9.9e-14	PFAM
Pfam:Pkinase_Tyr	593	750	5.2e-32	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000202161

SMART Domains

Protein: ENSMUSP00000144485
Gene: ENSMUSG00000029231

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
Blast:IG	34	88	5e-32	BLAST

Predicted Effect

probably damaging
Transcript: ENSMUST00000202186
AA Change: N240T

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

SMART Domains

Protein: ENSMUSP00000144543
Gene: ENSMUSG00000029231
AA Change: N240T

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
IG	34	122	2.6e-5	SMART
IG_like	135	206	7e-2	SMART
IGc2	226	297	3.6e-6	SMART
IG	322	414	1.2e-2	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000202681
AA Change: N240T

PolyPhen 2 Score 0.424 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000143906
Gene: ENSMUSG00000029231
AA Change: N240T

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
IG	34	122	6.07e-3	SMART
IG_like	135	206	1.7e1	SMART
IGc2	226	297	8.72e-4	SMART
IG	322	414	2.86e0	SMART
transmembrane domain	527	549	N/A	INTRINSIC
Pfam:Pkinase	593	701	9.9e-14	PFAM
Pfam:Pkinase_Tyr	593	750	5.2e-32	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000202992

SMART Domains

Protein: ENSMUSP00000144132
Gene: ENSMUSG00000029231

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
IG	34	122	2.6e-5	SMART

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.5%

Validation Efficiency

MGI Phenotype

FUNCTION: This gene encodes a member of the receptor tyrosine kinase family of proteins. Binding of platelet-derived growth factor protein ligands to this receptor triggers receptor dimerization and autophosphorylation, resulting in the activation of several downstream signaling pathways. Signaling through the encoded receptor plays a role in gastrulation and the development of nearly all organ systems. Mice lacking a functional copy of this gene reportedly exhibit defects in lung, skeleton, testis and the central nervous system, and die soon after birth. Alternative splicing and intronic polyadenylation of gene transcripts have been implicated in muscle regeneration and fibrosis in adult mice. [provided by RefSeq, Jan 2017]
PHENOTYPE: Homozygotes for targeted null mutations exhibit incomplete cephalic closure, increased apoptosis of neural crest cells, impaired myotome and testis formation, abnormal mucosal linings, thoracic skeletal defects, and midgestational lethality. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc6	A	T	7: 46,016,468	W243R	probably damaging	Het
Ablim1	T	G	19: 57,239,180	K18Q	probably benign	Het
Adamts18	T	A	8: 113,777,938	N174Y	possibly damaging	Het
Agbl2	A	G	2: 90,784,093	H23R	probably benign	Het
Akap6	T	G	12: 53,010,552	Y934D	probably damaging	Het
Alas1	C	T	9: 106,234,062	S635N	probably benign	Het
Ankrd24	A	G	10: 81,642,299		probably null	Het
Atp6v0a4	A	G	6: 38,060,982	L560P	probably damaging	Het
Cacng1	C	T	11: 107,716,292	V34M	possibly damaging	Het
Clcn3	C	T	8: 60,934,517	A233T	probably damaging	Het
Cntnap3	A	G	13: 64,799,135	F160S	probably damaging	Het
Ctnnd2	A	G	15: 30,881,130	S719G	probably damaging	Het
Exosc2	G	A	2: 31,674,743	V107I	probably benign	Het
Fam83b	C	A	9: 76,491,803	V673F	probably benign	Het
Fras1	T	C	5: 96,780,070	F3781L	probably damaging	Het
Gal3st1	T	A	11: 3,998,660	L289H	probably damaging	Het
Garem1	T	C	18: 21,148,313	I329V	probably benign	Het
Gli3	G	A	13: 15,725,711	G1228S	possibly damaging	Het
Gpbp1l1	T	C	4: 116,574,361	F72S	possibly damaging	Het
Hao1	T	A	2: 134,548,261	M53L	probably benign	Het
Hjurp	CTCTGGGAGGGCTTGCTCCGGGGGCAGTGTGTCCTGTTCTTGTGCAGCCCCT	C	1: 88,266,277		probably benign	Het
Iqcm	A	G	8: 75,753,455	E347G	probably damaging	Het
Itpr3	G	A	17: 27,118,677		probably benign	Het
Kcnrg	A	G	14: 61,607,657	I49V	possibly damaging	Het
Lrrc8e	G	A	8: 4,235,346	G524S	probably benign	Het
Lrrn1	A	T	6: 107,568,300	Y353F	probably damaging	Het
Mdn1	A	G	4: 32,739,849	D3701G	possibly damaging	Het
Mtmr2	A	G	9: 13,805,471	T623A	probably benign	Het
Ndst4	C	A	3: 125,714,647	S287*	probably null	Het
Ntrk3	A	C	7: 78,302,732	M579R	probably benign	Het
Oas1a	G	A	5: 120,899,254	L237F	probably damaging	Het
Olfr1350	A	T	7: 6,570,819	Y276F	probably damaging	Het
Olfr169	T	C	16: 19,566,520	D121G	probably benign	Het
Olfr857	T	C	9: 19,713,643	M272T	probably benign	Het
Paqr5	T	A	9: 61,956,225	I272F	probably damaging	Het
Pcdha11	T	A	18: 37,007,538	V740E	probably damaging	Het
Plbd2	G	A	5: 120,494,380	Q186*	probably null	Het
Plce1	G	A	19: 38,777,893	E2121K	possibly damaging	Het
Ppargc1a	C	A	5: 51,495,738	G161C	probably damaging	Het
Ptprk	T	C	10: 28,334,480	I166T	possibly damaging	Het
Rhox8	GCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT	GCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCT	X: 37,878,114		probably benign	Het
Rpap2	T	A	5: 107,620,589	L431Q	probably damaging	Het
Rslcan18	T	A	13: 67,102,064	K160*	probably null	Het
Sema7a	T	C	9: 57,954,905	F180L	probably benign	Het
Sh2d3c	C	T	2: 32,753,027	L741F	probably damaging	Het
Shank1	G	A	7: 44,312,918	S71N	unknown	Het
Skint6	C	T	4: 112,806,840		probably null	Het
Skiv2l	A	T	17: 34,841,102	D897E	probably benign	Het
Slc35f3	T	C	8: 126,382,254	S181P	probably damaging	Het
Slc4a9	A	T	18: 36,529,216	E127V	probably null	Het
Spata5	T	C	3: 37,431,909	V260A	probably benign	Het
Speg	C	T	1: 75,388,091	T372I	probably damaging	Het
Syce1l	A	G	8: 113,655,103	T204A	probably benign	Het
Tas2r138	T	A	6: 40,612,458	M285L	probably benign	Het
Tbc1d10a	G	C	11: 4,213,604	K285N	probably damaging	Het
Trim9	T	A	12: 70,346,454	M239L	probably benign	Het
Trp53bp1	A	G	2: 121,209,280	S1293P	probably benign	Het
Uaca	C	T	9: 60,872,216	T1295M	possibly damaging	Het
Ubald1	G	T	16: 4,875,569	Q161K	possibly damaging	Het
Ugt1a10	C	T	1: 88,216,260	R201C	probably damaging	Het
Vps45	T	G	3: 96,042,925	T231P	probably damaging	Het
Wdr17	A	T	8: 54,635,477	D1186E	probably benign	Het
Zfp534	G	A	4: 147,682,274	T8I	probably benign	Het
Zfp68	T	C	5: 138,607,255	N269D	probably benign	Het

Other mutations in Pdgfra

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00489:Pdgfra	APN	5	75163679	missense	probably benign	0.40
IGL00574:Pdgfra	APN	5	75181047	missense	probably damaging	1.00
IGL00906:Pdgfra	APN	5	75180173	missense	probably benign	0.00
IGL00964:Pdgfra	APN	5	75175065	missense	probably damaging	1.00
IGL01467:Pdgfra	APN	5	75185631	critical splice donor site	probably null
IGL01485:Pdgfra	APN	5	75163652	missense	probably benign	0.02
IGL01556:Pdgfra	APN	5	75177691	missense	probably damaging	1.00
IGL01949:Pdgfra	APN	5	75170665	missense	probably damaging	0.98
IGL02066:Pdgfra	APN	5	75170580	missense	possibly damaging	0.55
IGL02271:Pdgfra	APN	5	75187906	missense	probably damaging	1.00
IGL02726:Pdgfra	APN	5	75194957	nonsense	probably null
IGL02858:Pdgfra	APN	5	75194974	missense	probably damaging	1.00
IGL03306:Pdgfra	APN	5	75192533	missense	possibly damaging	0.49
Pony_express	UTSW	5	75189234	nonsense	probably null
P0033:Pdgfra	UTSW	5	75192561	missense	probably damaging	1.00
PIT4472001:Pdgfra	UTSW	5	75180246	missense	probably damaging	1.00
R0134:Pdgfra	UTSW	5	75166511	missense	probably damaging	1.00
R0200:Pdgfra	UTSW	5	75163777	missense	probably damaging	1.00
R0254:Pdgfra	UTSW	5	75167935	missense	probably damaging	1.00
R0331:Pdgfra	UTSW	5	75195052	missense	probably damaging	1.00
R0467:Pdgfra	UTSW	5	75195036	missense	probably damaging	1.00
R0532:Pdgfra	UTSW	5	75170773	missense	probably benign	0.00
R0608:Pdgfra	UTSW	5	75163777	missense	probably damaging	1.00
R0765:Pdgfra	UTSW	5	75187987	unclassified	probably benign
R1171:Pdgfra	UTSW	5	75173447	missense	probably damaging	0.98
R1372:Pdgfra	UTSW	5	75189263	missense	probably damaging	0.96
R1530:Pdgfra	UTSW	5	75189010	splice site	probably null
R1585:Pdgfra	UTSW	5	75192603	missense	probably damaging	1.00
R1666:Pdgfra	UTSW	5	75189020	missense	possibly damaging	0.94
R1836:Pdgfra	UTSW	5	75183014	missense	possibly damaging	0.95
R1868:Pdgfra	UTSW	5	75170873	missense	probably benign	0.43
R1923:Pdgfra	UTSW	5	75163733	missense	probably benign	0.03
R2075:Pdgfra	UTSW	5	75187948	missense	probably damaging	1.00
R2261:Pdgfra	UTSW	5	75185523	missense	probably benign	0.03
R2262:Pdgfra	UTSW	5	75185523	missense	probably benign	0.03
R3028:Pdgfra	UTSW	5	75174981	missense	probably damaging	1.00
R3236:Pdgfra	UTSW	5	75167936	missense	probably damaging	1.00
R3692:Pdgfra	UTSW	5	75189287	missense	possibly damaging	0.54
R3701:Pdgfra	UTSW	5	75180220	nonsense	probably null
R3890:Pdgfra	UTSW	5	75167927	missense	probably null	0.57
R3901:Pdgfra	UTSW	5	75192508	missense	probably benign	0.10
R3902:Pdgfra	UTSW	5	75192508	missense	probably benign	0.10
R4272:Pdgfra	UTSW	5	75183070	missense	probably benign	0.05
R4532:Pdgfra	UTSW	5	75181083	missense	probably damaging	1.00
R4660:Pdgfra	UTSW	5	75162271	missense	possibly damaging	0.82
R4753:Pdgfra	UTSW	5	75181524	missense	probably damaging	1.00
R4795:Pdgfra	UTSW	5	75189311	missense	probably benign
R4796:Pdgfra	UTSW	5	75189311	missense	probably benign
R4884:Pdgfra	UTSW	5	75189312	missense	probably benign	0.07
R4936:Pdgfra	UTSW	5	75195026	missense	probably damaging	1.00
R5625:Pdgfra	UTSW	5	75189337	critical splice donor site	probably null
R5666:Pdgfra	UTSW	5	75173495	missense	probably benign	0.00
R5670:Pdgfra	UTSW	5	75173495	missense	probably benign	0.00
R5714:Pdgfra	UTSW	5	75186012	missense	probably damaging	1.00
R5836:Pdgfra	UTSW	5	75163774	missense	possibly damaging	0.52
R6126:Pdgfra	UTSW	5	75170529	missense	probably benign	0.09
R6141:Pdgfra	UTSW	5	75173396	missense	probably damaging	0.98
R6297:Pdgfra	UTSW	5	75173474	missense	possibly damaging	0.88
R6363:Pdgfra	UTSW	5	75170836	missense	possibly damaging	0.91
R6376:Pdgfra	UTSW	5	75166519	missense	probably benign	0.02
R6485:Pdgfra	UTSW	5	75175074	splice site	probably null
R6612:Pdgfra	UTSW	5	75167842	missense	probably benign	0.01
R6641:Pdgfra	UTSW	5	75162101	intron	probably benign
R6954:Pdgfra	UTSW	5	75173394	missense	possibly damaging	0.82
R7110:Pdgfra	UTSW	5	75189234	nonsense	probably null
R7192:Pdgfra	UTSW	5	75183106	missense	probably damaging	1.00
R7294:Pdgfra	UTSW	5	75181651	missense	probably benign	0.05
R7347:Pdgfra	UTSW	5	75183098	missense	possibly damaging	0.91
R7476:Pdgfra	UTSW	5	75170603	missense	probably damaging	1.00
R7512:Pdgfra	UTSW	5	75195014	nonsense	probably null
R7609:Pdgfra	UTSW	5	75166721	missense	probably benign	0.10
R7925:Pdgfra	UTSW	5	75192418	splice site	probably benign
R8141:Pdgfra	UTSW	5	75177726	missense	possibly damaging	0.81
R8490:Pdgfra	UTSW	5	75170668	critical splice donor site	probably null
R8886:Pdgfra	UTSW	5	75183073	missense	probably benign	0.03
R9234:Pdgfra	UTSW	5	75163601	missense	possibly damaging	0.93
R9339:Pdgfra	UTSW	5	75194974	missense	probably damaging	1.00
R9459:Pdgfra	UTSW	5	75192468	missense	probably damaging	1.00
R9519:Pdgfra	UTSW	5	75176689	missense	probably benign	0.00
Z1088:Pdgfra	UTSW	5	75166577	missense	probably benign	0.03
Z1177:Pdgfra	UTSW	5	75181674	missense	probably null	1.00

Predicted Primers

PCR Primer
(F):5'- TTTAACGGCCCTGATTCAGC -3'
(R):5'- ATGTCCCTTGTGGTCATGC -3'

Sequencing Primer
(F):5'- TTAACGGCCCTGATTCAGCTACAG -3'
(R):5'- GAGTCAAATGTGCCCATTGC -3'

Posted On

2022-06-15