Mutagenetix > Incidental Mutation

Incidental Mutation 'R7196:Prdm1'

559946

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

045275-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7196 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

44313173-44404497 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 44332988 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 44 (S44P)

Ref Sequence

ENSEMBL: ENSMUSP00000039248 (fasta)

Gene Model

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

AlphaFold

Q60636

Predicted Effect

probably benign
Transcript: ENSMUST00000039174
AA Change: S44P

PolyPhen 2 Score 0.137 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000039248
Gene: ENSMUSG00000038151
AA Change: S44P

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

SMART Domains

Protein: ENSMUSP00000101129
Gene: ENSMUSG00000038151

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

probably benign
Transcript: ENSMUST00000218369

Coding Region Coverage

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

Validation Efficiency

99% (94/95)

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: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700017B05Rik	AGCTTCCCTGCTT	AGCTT	9: 57,165,505 (GRCm39)		probably null	Het
4921504E06Rik	A	C	2: 19,498,806 (GRCm39)	S396A	probably benign	Het
Actr6	C	A	10: 89,550,784 (GRCm39)	V337F	possibly damaging	Het
Agtpbp1	T	C	13: 59,680,994 (GRCm39)	T73A	possibly damaging	Het
AI182371	A	T	2: 34,976,441 (GRCm39)		probably null	Het
Apob	A	G	12: 8,033,893 (GRCm39)	E202G	possibly damaging	Het
Asb4	A	T	6: 5,423,356 (GRCm39)	M168L	probably benign	Het
AU018091	T	C	7: 3,213,788 (GRCm39)	Y152C	probably damaging	Het
Casp3	G	A	8: 47,088,498 (GRCm39)	G132R	possibly damaging	Het
Cbfa2t3	C	A	8: 123,365,729 (GRCm39)	A229S	probably benign	Het
Cdh23	A	T	10: 60,143,759 (GRCm39)	Y2949N	probably damaging	Het
Ceacam3	T	C	7: 16,888,881 (GRCm39)	Y217H		Het
Cldn5	A	T	16: 18,595,630 (GRCm39)		probably benign	Het
Cltc	T	C	11: 86,597,657 (GRCm39)	D1093G	probably damaging	Het
Cnn3	G	A	3: 121,248,437 (GRCm39)		probably null	Het
Col4a2	A	G	8: 11,448,693 (GRCm39)	Y71C	probably damaging	Het
Csf1	T	C	3: 107,661,214 (GRCm39)	D77G	possibly damaging	Het
Cyp2j7	T	A	4: 96,103,651 (GRCm39)	T295S	probably benign	Het
Dnah7a	A	T	1: 53,724,000 (GRCm39)	M133K	probably benign	Het
Dock5	G	A	14: 67,993,919 (GRCm39)	P1852L	probably damaging	Het
Dpysl3	T	A	18: 43,462,910 (GRCm39)	D489V	probably damaging	Het
Dsg4	T	C	18: 20,599,537 (GRCm39)	Y718H	probably damaging	Het
Dync2h1	G	A	9: 7,147,715 (GRCm39)	Q972*	probably null	Het
Epn1	G	A	7: 5,096,380 (GRCm39)	D225N	possibly damaging	Het
Esp4	A	G	17: 40,913,256 (GRCm39)	E41G	probably benign	Het
Fam171a2	T	C	11: 102,329,172 (GRCm39)	D529G	probably benign	Het
Fbxl13	A	T	5: 21,691,301 (GRCm39)	I694N	probably damaging	Het
Fshr	C	T	17: 89,292,897 (GRCm39)	A594T	probably damaging	Het
Galnt3	A	G	2: 65,921,268 (GRCm39)	Y533H	probably damaging	Het
Gja5	C	A	3: 96,958,422 (GRCm39)	R160S	probably damaging	Het
Gm12353	A	T	4: 19,608,938 (GRCm39)	D7V	unknown	Het
Gm17669	T	C	18: 67,695,572 (GRCm39)	F39S	probably damaging	Het
Gm7145	T	A	1: 117,913,791 (GRCm39)	N224K	possibly damaging	Het
Gpd1	G	T	15: 99,619,936 (GRCm39)	G245C	probably benign	Het
Gpr4	G	A	7: 18,957,089 (GRCm39)	G337D	probably benign	Het
Hgd	G	A	16: 37,409,078 (GRCm39)	C14Y	probably benign	Het
Ibtk	A	T	9: 85,625,709 (GRCm39)	S14T	probably damaging	Het
Ifi205	G	T	1: 173,854,109 (GRCm39)	N181K	probably damaging	Het
Inppl1	G	A	7: 101,477,993 (GRCm39)	A673V	probably benign	Het
Itgb3	C	A	11: 104,524,438 (GRCm39)	Y191*	probably null	Het
Jrkl	G	T	9: 13,244,162 (GRCm39)	P500T	probably benign	Het
Kcnq1	G	A	7: 142,912,478 (GRCm39)	V515I	possibly damaging	Het
Kifc3	A	G	8: 95,833,239 (GRCm39)	V453A	probably benign	Het
Krt10	C	T	11: 99,278,371 (GRCm39)	E263K	probably damaging	Het
Lingo1	A	T	9: 56,527,903 (GRCm39)	F235I	probably damaging	Het
Lmo7	T	A	14: 102,133,936 (GRCm39)	D660E	possibly damaging	Het
Magi3	A	C	3: 103,956,484 (GRCm39)	C661W	probably benign	Het
Mmp1a	C	T	9: 7,476,018 (GRCm39)	Q428*	probably null	Het
Msrb1	A	T	17: 24,958,556 (GRCm39)	T47S	probably benign	Het
Naip6	A	T	13: 100,436,666 (GRCm39)	I619K	probably benign	Het
Ndfip2	T	C	14: 105,535,472 (GRCm39)	S253P	probably damaging	Het
Nebl	A	T	2: 17,457,329 (GRCm39)	V77E	probably damaging	Het
Nit1	T	C	1: 171,172,003 (GRCm39)	E65G	probably benign	Het
Ntn4	C	T	10: 93,569,576 (GRCm39)	H430Y	probably benign	Het
Nxpe5	A	T	5: 138,237,586 (GRCm39)	I49F	probably benign	Het
Or10a2	A	G	7: 106,673,935 (GRCm39)	N300S	probably benign	Het
Or10c1	A	G	17: 37,522,084 (GRCm39)	I220T	probably damaging	Het
Or14c46	A	T	7: 85,918,649 (GRCm39)	M116K	probably damaging	Het
Or1e23	A	G	11: 73,407,957 (GRCm39)	Y23H	probably benign	Het
Or1m1	A	T	9: 18,666,886 (GRCm39)	L15*	probably null	Het
Or4k49	T	G	2: 111,495,042 (GRCm39)	L157W	probably damaging	Het
Or52s6	A	T	7: 103,092,204 (GRCm39)	M42K	probably benign	Het
Or7e178	A	G	9: 20,225,494 (GRCm39)	Y241H	probably benign	Het
Oxct2a	T	A	4: 123,217,165 (GRCm39)	N72I	probably damaging	Het
Pappa	G	A	4: 65,242,128 (GRCm39)		probably null	Het
Pcnx1	G	A	12: 82,042,312 (GRCm39)	R34H	possibly damaging	Het
Plekha5	G	T	6: 140,489,648 (GRCm39)	V236L	possibly damaging	Het
Prss46	T	A	9: 110,680,533 (GRCm39)	L226Q	probably benign	Het
Prss47	C	A	13: 65,192,640 (GRCm39)	W380C	probably benign	Het
Ptch2	T	G	4: 116,971,946 (GRCm39)	V1156G	probably benign	Het
Rab3gap2	T	C	1: 185,013,864 (GRCm39)	F1190S	probably damaging	Het
Raver2	T	G	4: 100,960,056 (GRCm39)	Y179D	probably damaging	Het
Rgl2	C	T	17: 34,152,403 (GRCm39)	R367W	probably damaging	Het
Ripor2	T	G	13: 24,888,808 (GRCm39)	I629S	possibly damaging	Het
Robo4	T	A	9: 37,314,001 (GRCm39)	M84K	possibly damaging	Het
Rps6ka5	A	T	12: 100,562,123 (GRCm39)	S252T	possibly damaging	Het
Rtl1	C	T	12: 109,559,221 (GRCm39)	V873M	possibly damaging	Het
Sla	T	A	15: 66,703,420 (GRCm39)	R4W	probably benign	Het
Smco1	A	G	16: 32,092,620 (GRCm39)	D97G	probably damaging	Het
Srgap1	T	C	10: 121,676,753 (GRCm39)	T414A	probably benign	Het
Syt14	A	G	1: 192,717,936 (GRCm39)	I3T	probably benign	Het
Tnpo2	G	A	8: 85,773,766 (GRCm39)	V303M	possibly damaging	Het
Tstd2	A	C	4: 46,119,955 (GRCm39)	S332R	probably damaging	Het
Ttn	C	A	2: 76,582,386 (GRCm39)	A22836S	possibly damaging	Het
Ufl1	A	G	4: 25,250,669 (GRCm39)	V728A	probably benign	Het
Usp33	A	T	3: 152,089,828 (GRCm39)	K789N	possibly damaging	Het
Usp54	T	A	14: 20,638,438 (GRCm39)	Q214L	probably damaging	Het
Vmn2r7	T	G	3: 64,623,198 (GRCm39)	N374T	probably benign	Het
Zbtb7a	T	A	10: 80,980,434 (GRCm39)	N209K	probably damaging	Het
Zc3hav1	A	G	6: 38,306,207 (GRCm39)	V615A	probably benign	Het
Zdhhc20	A	G	14: 58,111,348 (GRCm39)		probably null	Het
Zfp90	G	T	8: 107,151,780 (GRCm39)	V498L	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
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
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
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'- TGTCCACAAAGTCATATCAGCG -3'
(R):5'- GCGCCCACAACACATTTCTG -3'

Sequencing Primer
(F):5'- AAGTCATATCAGCGTCCTCCATG -3'
(R):5'- TCTCTCCCGATGAGGTTA -3'

Posted On

2019-06-26