Mutagenetix > Incidental Mutation

Incidental Mutation 'R2070:Prdm1'

227063

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

040075-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2070 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

44313173-44404497 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 44317408 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Asparagine at position 505 (D505N)

Ref Sequence

ENSEMBL: ENSMUSP00000039248 (fasta)

Gene Model

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

AlphaFold

Q60636

Predicted Effect

possibly damaging
Transcript: ENSMUST00000039174
AA Change: D505N

PolyPhen 2 Score 0.816 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000039248
Gene: ENSMUSG00000038151
AA Change: D505N

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

possibly damaging
Transcript: ENSMUST00000105490
AA Change: D472N

PolyPhen 2 Score 0.628 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000101129
Gene: ENSMUSG00000038151
AA Change: D472N

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

possibly damaging
Transcript: ENSMUST00000218369
AA Change: D487N

PolyPhen 2 Score 0.811 (Sensitivity: 0.84; Specificity: 0.93)

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.5%

Validation Efficiency

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2810021J22Rik	A	G	11: 58,767,595 (GRCm39)	K31E	probably damaging	Het
Abcc10	G	C	17: 46,614,491 (GRCm39)	N1477K	probably benign	Het
Ablim2	G	A	5: 35,955,857 (GRCm39)	C24Y	probably damaging	Het
Ankle1	T	C	8: 71,861,988 (GRCm39)	F497S	probably damaging	Het
Armh3	G	T	19: 45,879,724 (GRCm39)	P543Q	probably damaging	Het
Ash1l	C	G	3: 88,873,510 (GRCm39)	P98A	probably damaging	Het
Atad5	A	T	11: 79,988,878 (GRCm39)		probably null	Het
B3gnt4	A	T	5: 123,649,433 (GRCm39)	H266L	probably benign	Het
Bmi1	A	G	2: 18,688,851 (GRCm39)	I207V	probably benign	Het
Bnip3l	A	G	14: 67,226,671 (GRCm39)	M174T	probably damaging	Het
Bora	T	C	14: 99,299,714 (GRCm39)	S229P	probably damaging	Het
Ccdc121	T	C	5: 31,644,727 (GRCm39)	V160A	possibly damaging	Het
Ccdc27	T	A	4: 154,126,270 (GRCm39)	N73I	unknown	Het
Cdc42bpg	T	A	19: 6,370,518 (GRCm39)	C1204S	probably damaging	Het
Cdsn	A	T	17: 35,865,591 (GRCm39)	D40V	probably damaging	Het
Cilp	T	A	9: 65,186,377 (GRCm39)	V824D	probably damaging	Het
Cmtr1	A	G	17: 29,913,757 (GRCm39)		probably null	Het
Cntnap1	A	G	11: 101,073,805 (GRCm39)	Y652C	probably damaging	Het
Col12a1	T	C	9: 79,554,978 (GRCm39)	I2033M	probably benign	Het
Cwh43	T	C	5: 73,578,860 (GRCm39)	L289P	probably damaging	Het
Ddhd1	T	C	14: 45,848,081 (GRCm39)	D529G	probably damaging	Het
Defb28	T	A	2: 152,362,064 (GRCm39)	S75T	probably benign	Het
Dennd2a	A	T	6: 39,442,053 (GRCm39)	V939D	probably damaging	Het
Dlg5	T	C	14: 24,186,703 (GRCm39)	R1866G	probably damaging	Het
Dsc1	C	T	18: 20,221,353 (GRCm39)		probably null	Het
Ecscr	T	G	18: 35,848,490 (GRCm39)	N184T	probably damaging	Het
Eif4ebp1	G	T	8: 27,763,372 (GRCm39)	R55L	probably damaging	Het
Eml1	G	T	12: 108,479,258 (GRCm39)	V344L	probably damaging	Het
Exoc2	G	T	13: 30,999,353 (GRCm39)	N901K	probably benign	Het
Fam161b	T	A	12: 84,403,202 (GRCm39)	I143F	probably benign	Het
Fam180a	A	G	6: 35,302,846 (GRCm39)	S2P	probably benign	Het
Fat3	T	A	9: 15,910,666 (GRCm39)	I1779F	probably benign	Het
Fat4	A	G	3: 39,064,804 (GRCm39)	K4920R	probably benign	Het
Fsip2	T	A	2: 82,806,699 (GRCm39)	V1006E	probably damaging	Het
Glcci1	A	G	6: 8,558,566 (GRCm39)	S30G	probably damaging	Het
Gm5414	A	T	15: 101,536,495 (GRCm39)	S43R	possibly damaging	Het
Hao1	T	C	2: 134,372,535 (GRCm39)	T158A	probably damaging	Het
Hic1	T	C	11: 75,059,885 (GRCm39)	H154R	possibly damaging	Het
Hmgxb3	T	C	18: 61,304,431 (GRCm39)	Y53C	probably damaging	Het
Ipmk	A	T	10: 71,208,579 (GRCm39)	K122*	probably null	Het
Jakmip2	T	C	18: 43,696,395 (GRCm39)	E518G	probably benign	Het
Kmt2e	A	G	5: 23,706,993 (GRCm39)	T1519A	probably benign	Het
Lfng	T	C	5: 140,598,350 (GRCm39)	I224T	possibly damaging	Het
Magel2	G	A	7: 62,028,844 (GRCm39)	V583I	unknown	Het
Map4k5	C	T	12: 69,863,111 (GRCm39)	V629I	probably damaging	Het
Med12l	A	G	3: 59,152,326 (GRCm39)	D1037G	probably damaging	Het
Morc1	C	T	16: 48,412,974 (GRCm39)	T705I	probably benign	Het
Mptx2	A	T	1: 173,102,145 (GRCm39)	Y181*	probably null	Het
Mrpl24	T	C	3: 87,830,374 (GRCm39)		probably null	Het
Myo5a	A	G	9: 75,089,266 (GRCm39)	E1132G	probably benign	Het
Nedd4l	T	G	18: 65,345,891 (GRCm39)	F814L	probably damaging	Het
Nmral1	T	A	16: 4,534,211 (GRCm39)	I77F	probably damaging	Het
Oit3	T	G	10: 59,266,835 (GRCm39)	I224L	probably benign	Het
Oxsm	A	G	14: 16,241,983 (GRCm38)	L262P	probably benign	Het
Pacs2	C	T	12: 113,024,731 (GRCm39)	T407I	probably damaging	Het
Pard6g	T	C	18: 80,160,940 (GRCm39)	I351T	probably benign	Het
Pdcl2	A	T	5: 76,472,838 (GRCm39)		probably null	Het
Pdzph1	T	C	17: 59,281,092 (GRCm39)	R397G	probably benign	Het
Phip	T	A	9: 82,757,352 (GRCm39)	I1607L	probably benign	Het
Plekhd1	C	A	12: 80,739,681 (GRCm39)	S10*	probably null	Het
Pramel24	T	G	4: 143,453,472 (GRCm39)	Y193*	probably null	Het
Psmd13	T	C	7: 140,477,561 (GRCm39)	V320A	probably damaging	Het
Rbak	A	G	5: 143,162,339 (GRCm39)	L8P	probably damaging	Het
Rere	C	A	4: 150,699,047 (GRCm39)		probably benign	Het
Rint1	T	C	5: 24,015,927 (GRCm39)	S456P	possibly damaging	Het
Scn3a	T	C	2: 65,351,210 (GRCm39)	Q446R	possibly damaging	Het
Slitrk5	A	G	14: 111,917,621 (GRCm39)	Y415C	probably damaging	Het
Snrnp200	A	G	2: 127,054,323 (GRCm39)	E210G	possibly damaging	Het
Snrnp200	A	G	2: 127,079,803 (GRCm39)	T1891A	probably benign	Het
Sohlh2	A	G	3: 55,115,043 (GRCm39)	I343V	probably benign	Het
Spin1	T	C	13: 51,298,573 (GRCm39)		probably null	Het
St14	T	A	9: 31,002,669 (GRCm39)	I745F	probably damaging	Het
Sv2a	G	A	3: 96,101,191 (GRCm39)	A730T	possibly damaging	Het
Tars2	C	A	3: 95,654,950 (GRCm39)	G113C	probably damaging	Het
Tlcd3b	T	C	7: 126,419,012 (GRCm39)	L4P	probably benign	Het
Trp53	A	G	11: 69,480,458 (GRCm39)	D278G	probably damaging	Het
Ubxn7	T	A	16: 32,191,287 (GRCm39)	C160S	possibly damaging	Het
Uty	T	C	Y: 1,169,193 (GRCm39)	E414G	probably benign	Het
Wrap73	T	A	4: 154,233,200 (GRCm39)	S125T	possibly damaging	Het
Wwc2	T	C	8: 48,321,356 (GRCm39)	D586G	unknown	Het
Zfp106	T	C	2: 120,354,010 (GRCm39)	H1490R	probably benign	Het
Zswim5	T	C	4: 116,837,109 (GRCm39)	V731A	probably benign	Het
Zyg11b	G	C	4: 108,108,016 (GRCm39)	N463K	possibly 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
R1438:Prdm1	UTSW	10	44,318,124 (GRCm39)	missense	probably benign	0.00
R1519:Prdm1	UTSW	10	44,315,982 (GRCm39)	nonsense	probably null
R1886:Prdm1	UTSW	10	44,315,754 (GRCm39)	missense	probably damaging	0.99
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'- ATGAGATTCATGGCTCCGTCAG -3'
(R):5'- CACCGTACGGCATTAGTTCC -3'

Sequencing Primer
(F):5'- GCCATCACTGATGAGGTAGC -3'
(R):5'- ACGGCATTAGTTCCAATGGC -3'

Posted On

2014-09-17