Mutagenetix > Incidental Mutation

Incidental Mutation 'R1438:Prdm1'

160782

Institutional Source

Beutler Lab

Gene Symbol

Prdm1

Ensembl Gene

ENSMUSG00000038151

Gene Name

PR domain containing 1, with ZNF domain

Synonyms

Blimp-1, PRDI-BF1, Blimp1, b2b1765Clo

MMRRC Submission

039493-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1438 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

44313173-44404497 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 44318124 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 248 (E248G)

Ref Sequence

ENSEMBL: ENSMUSP00000151237 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000039174] [ENSMUST00000105490] [ENSMUST00000218369]

AlphaFold

Q60636

Predicted Effect

probably benign
Transcript: ENSMUST00000039174
AA Change: E266G

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

SMART Domains

Protein: ENSMUSP00000039248
Gene: ENSMUSG00000038151
AA Change: E266G

Domain	Start	End	E-Value	Type
SET	118	239	1.1e-19	SMART
low complexity region	359	393	N/A	INTRINSIC
low complexity region	541	556	N/A	INTRINSIC
ZnF_C2H2	606	628	6.42e-4	SMART
ZnF_C2H2	634	656	3.89e-3	SMART
ZnF_C2H2	662	684	7.26e-3	SMART
ZnF_C2H2	690	712	1.36e-2	SMART
ZnF_C2H2	718	738	1.12e2	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000105490
AA Change: E233G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000101129
Gene: ENSMUSG00000038151
AA Change: E233G

Domain	Start	End	E-Value	Type
SET	85	206	1.1e-19	SMART
low complexity region	326	360	N/A	INTRINSIC
low complexity region	508	523	N/A	INTRINSIC
ZnF_C2H2	573	595	6.42e-4	SMART
ZnF_C2H2	601	623	3.89e-3	SMART
ZnF_C2H2	629	651	7.26e-3	SMART
ZnF_C2H2	657	679	1.36e-2	SMART
ZnF_C2H2	685	705	1.12e2	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000167340

Predicted Effect

probably benign
Transcript: ENSMUST00000218369
AA Change: E248G

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

Meta Mutation Damage Score

0.0734

Coding Region Coverage

1x: 98.9%
3x: 97.9%
10x: 94.7%
20x: 87.3%

Validation Efficiency

99% (80/81)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that acts as a repressor of beta-interferon gene expression. The protein binds specifically to the PRDI (positive regulatory domain I element) of the beta-IFN gene promoter. Transcription of this gene increases upon virus induction. Two alternatively spliced transcript variants that encode different isoforms have been reported. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous null mice display embryonic lethality and impaired primordial germ cell development, while heterozygotes display a decreased numbers of primordial germ cells but normal migration. Conditional mutants display impaired plasma cell and pre-plasmamemory B cell development. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Actl6b	A	T	5: 137,552,871 (GRCm39)	I67F	probably damaging	Het
Adam24	A	T	8: 41,134,431 (GRCm39)	N633I	probably benign	Het
Adgrg6	T	C	10: 14,344,585 (GRCm39)	S123G	possibly damaging	Het
Afdn	T	A	17: 14,075,652 (GRCm39)	F940L	probably damaging	Het
Ahrr	A	T	13: 74,372,987 (GRCm39)	Y26*	probably null	Het
Akap1	C	A	11: 88,735,577 (GRCm39)	G362*	probably null	Het
Aox3	A	T	1: 58,192,337 (GRCm39)	T536S	probably benign	Het
Boc	A	T	16: 44,309,109 (GRCm39)		probably null	Het
Cchcr1	T	C	17: 35,841,457 (GRCm39)		probably null	Het
Cct2	A	T	10: 116,890,897 (GRCm39)		probably benign	Het
Cd84	A	T	1: 171,679,685 (GRCm39)	Y121F	probably damaging	Het
Cecr2	T	A	6: 120,738,433 (GRCm39)	C275*	probably null	Het
Chchd3	C	A	6: 32,985,503 (GRCm39)		probably benign	Het
Ckmt2	A	T	13: 92,007,971 (GRCm39)		probably benign	Het
Col5a3	T	C	9: 20,691,253 (GRCm39)	K1131E	probably damaging	Het
Dek	A	T	13: 47,241,647 (GRCm39)	S306T	probably benign	Het
Dhx32	T	C	7: 133,339,069 (GRCm39)	E322G	possibly damaging	Het
Dlg5	T	A	14: 24,204,673 (GRCm39)	D941V	possibly damaging	Het
Dnah10	A	G	5: 124,876,009 (GRCm39)	N2559S	probably benign	Het
Dnajc3	A	G	14: 119,205,518 (GRCm39)	T171A	probably benign	Het
Eftud2	G	T	11: 102,750,868 (GRCm39)	F308L	probably damaging	Het
Elp6	T	C	9: 110,143,123 (GRCm39)	F95S	probably damaging	Het
Emsy	C	T	7: 98,270,613 (GRCm39)	V450I	possibly damaging	Het
Exoc3	A	T	13: 74,338,298 (GRCm39)	M362K	probably damaging	Het
Fat2	A	T	11: 55,178,637 (GRCm39)	D1474E	probably damaging	Het
Fcgbp	T	A	7: 27,803,158 (GRCm39)	C1587*	probably null	Het
Fosl2	T	A	5: 32,304,329 (GRCm39)	L88Q	probably damaging	Het
Fsd2	T	C	7: 81,198,621 (GRCm39)	D381G	probably benign	Het
Golim4	A	C	3: 75,863,440 (GRCm39)	S56A	probably damaging	Het
Gpr39	T	C	1: 125,800,093 (GRCm39)		probably benign	Het
Gucy1b2	T	C	14: 62,651,770 (GRCm39)	I409V	probably damaging	Het
Hivep1	A	G	13: 42,311,596 (GRCm39)	T1279A	probably benign	Het
Ifit1bl2	T	A	19: 34,596,569 (GRCm39)	Q349L	possibly damaging	Het
Kcnc1	A	T	7: 46,077,691 (GRCm39)	I498F	possibly damaging	Het
Kctd21	T	A	7: 96,996,704 (GRCm39)	I59N	probably damaging	Het
Lama5	T	A	2: 179,824,593 (GRCm39)	T2577S	probably benign	Het
Mief2	G	T	11: 60,621,140 (GRCm39)	R9M	possibly damaging	Het
Mmp3	T	C	9: 7,453,705 (GRCm39)	V442A	probably benign	Het
Nkapd1	C	A	9: 50,518,972 (GRCm39)	K213N	possibly damaging	Het
Nrxn3	C	T	12: 90,298,909 (GRCm39)	R477W	probably damaging	Het
Or12e7	A	G	2: 87,288,336 (GRCm39)	T276A	probably benign	Het
Or7a41	T	A	10: 78,871,122 (GRCm39)	V164E	possibly damaging	Het
Parp1	A	G	1: 180,418,807 (GRCm39)	T656A	probably benign	Het
Pcdhb19	A	G	18: 37,631,015 (GRCm39)	D270G	probably damaging	Het
Phlpp1	A	G	1: 106,101,142 (GRCm39)	D470G	possibly damaging	Het
Prtg	C	T	9: 72,818,032 (GRCm39)		probably benign	Het
Ptpn1	T	C	2: 167,818,529 (GRCm39)	Y424H	probably damaging	Het
Ptprr	T	C	10: 116,092,109 (GRCm39)	V369A	probably damaging	Het
Rai1	T	G	11: 60,076,221 (GRCm39)	V95G	probably benign	Het
Rasal3	T	A	17: 32,612,509 (GRCm39)		probably null	Het
Rbm19	A	G	5: 120,260,961 (GRCm39)	E195G	probably benign	Het
Rhbdd3	T	A	11: 5,053,332 (GRCm39)	L44Q	probably damaging	Het
Ripply2	T	C	9: 86,901,713 (GRCm39)	W80R	probably damaging	Het
Rnf183	A	G	4: 62,346,760 (GRCm39)	C13R	probably damaging	Het
Rorb	A	G	19: 18,932,417 (GRCm39)	L367P	probably damaging	Het
Rpl7a-ps5	C	T	17: 58,146,135 (GRCm39)		probably benign	Het
Rreb1	A	G	13: 38,114,581 (GRCm39)	N647D	probably benign	Het
Rtn1	A	T	12: 72,351,187 (GRCm39)	S341T	probably damaging	Het
Ryr3	T	C	2: 112,588,046 (GRCm39)	S2632G	probably benign	Het
Scube1	A	G	15: 83,499,227 (GRCm39)	C633R	possibly damaging	Het
Sdk1	A	T	5: 142,024,078 (GRCm39)	I723F	probably damaging	Het
Sec23a	A	T	12: 59,048,796 (GRCm39)	C109S	probably damaging	Het
Septin11	T	C	5: 93,296,287 (GRCm39)	F60L	probably damaging	Het
Sgf29	G	A	7: 126,271,063 (GRCm39)		probably null	Het
Skint5	A	G	4: 113,413,308 (GRCm39)		probably benign	Het
Smo	G	A	6: 29,755,482 (GRCm39)	V385I	possibly damaging	Het
Tada2a	G	A	11: 84,000,837 (GRCm39)	T76I	probably damaging	Het
Tas2r118	T	A	6: 23,969,422 (GRCm39)	H213L	possibly damaging	Het
Thoc5	A	T	11: 4,861,427 (GRCm39)		probably benign	Het
Tmem33	T	A	5: 67,424,634 (GRCm39)		probably null	Het
Top1mt	A	G	15: 75,546,247 (GRCm39)	L78P	probably damaging	Het
Uvssa	T	A	5: 33,571,228 (GRCm39)		probably benign	Het
Vmn2r50	A	T	7: 9,784,062 (GRCm39)	C137*	probably null	Het
Vmn2r81	A	G	10: 79,129,691 (GRCm39)	T861A	probably benign	Het
Wnt3	A	T	11: 103,699,077 (GRCm39)	N61I	probably damaging	Het
Zswim9	A	G	7: 13,011,144 (GRCm39)	I68T	possibly damaging	Het
Zzef1	T	C	11: 72,803,771 (GRCm39)	I2535T	probably damaging	Het

Other mutations in Prdm1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00657:Prdm1	APN	10	44,317,888 (GRCm39)	missense	probably damaging	1.00
IGL01331:Prdm1	APN	10	44,317,970 (GRCm39)	missense	possibly damaging	0.67
IGL02064:Prdm1	APN	10	44,317,338 (GRCm39)	missense	probably damaging	1.00
IGL02669:Prdm1	APN	10	44,315,880 (GRCm39)	missense	probably benign	0.28
IGL02944:Prdm1	APN	10	44,317,807 (GRCm39)	missense	probably benign
IGL03295:Prdm1	APN	10	44,315,866 (GRCm39)	missense	probably damaging	0.99
PIT4576001:Prdm1	UTSW	10	44,334,504 (GRCm39)	start codon destroyed	probably null	0.05
R0008:Prdm1	UTSW	10	44,317,675 (GRCm39)	missense	probably damaging	1.00
R0166:Prdm1	UTSW	10	44,316,087 (GRCm39)	missense	probably damaging	1.00
R0226:Prdm1	UTSW	10	44,332,692 (GRCm39)	missense	probably benign	0.03
R0284:Prdm1	UTSW	10	44,332,622 (GRCm39)	missense	probably damaging	1.00
R0398:Prdm1	UTSW	10	44,315,805 (GRCm39)	missense	probably damaging	1.00
R1200:Prdm1	UTSW	10	44,326,126 (GRCm39)	missense	probably damaging	1.00
R1405:Prdm1	UTSW	10	44,315,961 (GRCm39)	missense	probably damaging	1.00
R1405:Prdm1	UTSW	10	44,315,961 (GRCm39)	missense	probably damaging	1.00
R1519:Prdm1	UTSW	10	44,315,982 (GRCm39)	nonsense	probably null
R1886:Prdm1	UTSW	10	44,315,754 (GRCm39)	missense	probably damaging	0.99
R2070:Prdm1	UTSW	10	44,317,408 (GRCm39)	missense	possibly damaging	0.82
R2508:Prdm1	UTSW	10	44,322,803 (GRCm39)	missense	probably benign	0.37
R3087:Prdm1	UTSW	10	44,322,823 (GRCm39)	missense	probably damaging	1.00
R3150:Prdm1	UTSW	10	44,334,488 (GRCm39)	splice site	probably null
R4165:Prdm1	UTSW	10	44,317,572 (GRCm39)	missense	probably benign	0.11
R4490:Prdm1	UTSW	10	44,322,903 (GRCm39)	nonsense	probably null
R4647:Prdm1	UTSW	10	44,315,686 (GRCm39)	missense	probably damaging	0.98
R4911:Prdm1	UTSW	10	44,318,048 (GRCm39)	missense	possibly damaging	0.90
R4925:Prdm1	UTSW	10	44,316,165 (GRCm39)	missense	probably damaging	1.00
R5153:Prdm1	UTSW	10	44,326,221 (GRCm39)	missense	possibly damaging	0.94
R5247:Prdm1	UTSW	10	44,316,098 (GRCm39)	missense	probably damaging	1.00
R5792:Prdm1	UTSW	10	44,326,224 (GRCm39)	missense	probably damaging	1.00
R6164:Prdm1	UTSW	10	44,326,191 (GRCm39)	missense	probably damaging	1.00
R6247:Prdm1	UTSW	10	44,322,782 (GRCm39)	splice site	probably null
R7196:Prdm1	UTSW	10	44,332,988 (GRCm39)	missense	probably benign	0.14
R7270:Prdm1	UTSW	10	44,317,566 (GRCm39)	missense	probably benign	0.07
R7384:Prdm1	UTSW	10	44,334,503 (GRCm39)	missense	probably benign	0.01
R7822:Prdm1	UTSW	10	44,334,478 (GRCm39)	missense	probably benign	0.01
R8809:Prdm1	UTSW	10	44,315,749 (GRCm39)	missense	probably benign
R8827:Prdm1	UTSW	10	44,334,476 (GRCm39)	missense	probably benign	0.00
R8932:Prdm1	UTSW	10	44,317,335 (GRCm39)	missense	probably damaging	1.00
R8958:Prdm1	UTSW	10	44,316,729 (GRCm39)	missense	probably damaging	1.00
R9009:Prdm1	UTSW	10	44,322,997 (GRCm39)	missense	probably benign	0.02
R9020:Prdm1	UTSW	10	44,316,036 (GRCm39)	missense	probably damaging	1.00
R9176:Prdm1	UTSW	10	44,316,123 (GRCm39)	missense	probably damaging	1.00
R9378:Prdm1	UTSW	10	44,316,150 (GRCm39)	missense	probably damaging	1.00
R9471:Prdm1	UTSW	10	44,326,174 (GRCm39)	missense	probably damaging	1.00
R9535:Prdm1	UTSW	10	44,317,608 (GRCm39)	missense	probably damaging	1.00
R9554:Prdm1	UTSW	10	44,317,242 (GRCm39)	missense	probably benign	0.01
Z1088:Prdm1	UTSW	10	44,317,921 (GRCm39)	missense	probably damaging	1.00
Z1176:Prdm1	UTSW	10	44,322,829 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGGTGCCCGGATAGGATAAACCAC -3'
(R):5'- ACCCCATCTTAGTGAACGCTCTGC -3'

Sequencing Primer
(F):5'- CGGATAGGATAAACCACCCGAG -3'
(R):5'- ATTCCCGATcccccccc -3'

Posted On

2014-03-14