Mutagenetix > Incidental Mutation

Incidental Mutation 'R4925:Prdm1'

378973

Institutional Source

Beutler Lab

Gene Symbol

Prdm1

Ensembl Gene

ENSMUSG00000038151

Gene Name

PR domain containing 1, with ZNF domain

Synonyms

Blimp1, b2b1765Clo, Blimp-1, PRDI-BF1

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4925 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

44437177-44528501 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 44440169 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Phenylalanine at position 690 (Y690F)

Ref Sequence

ENSEMBL: ENSMUSP00000039248 (fasta)

Gene Model

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

AlphaFold

Q60636

Predicted Effect

probably damaging
Transcript: ENSMUST00000039174
AA Change: Y690F

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000039248
Gene: ENSMUSG00000038151
AA Change: Y690F

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: Y657F

PolyPhen 2 Score 0.896 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000101129
Gene: ENSMUSG00000038151
AA Change: Y657F

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: Y672F

PolyPhen 2 Score 0.851 (Sensitivity: 0.83; Specificity: 0.93)

Coding Region Coverage

1x: 98.9%
3x: 98.0%
10x: 95.0%
20x: 87.7%

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: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1810065E05Rik	T	A	11: 58,425,714	C173*	probably null	Het
2210407C18Rik	T	A	11: 58,610,687	T157S	probably damaging	Het
3425401B19Rik	T	A	14: 32,663,180	H276L	possibly damaging	Het
4930430A15Rik	T	C	2: 111,218,616	K273E	probably benign	Het
Adam21	T	G	12: 81,560,389	M200L	probably benign	Het
Adamts3	A	T	5: 89,684,323	S974T	probably benign	Het
Adamtsl3	T	A	7: 82,602,299		probably null	Het
Atp8b2	A	G	3: 89,946,623		probably null	Het
Brd8	T	C	18: 34,607,335	T552A	probably benign	Het
Btaf1	A	G	19: 37,011,333	S1826G	probably benign	Het
C330027C09Rik	T	C	16: 49,016,363		probably null	Het
Ccdc163	A	G	4: 116,711,331	E77G	possibly damaging	Het
Ces2g	A	G	8: 104,964,894	R194G	probably benign	Het
Cln8	A	G	8: 14,895,004	H106R	possibly damaging	Het
Col12a1	T	G	9: 79,674,795	L1391F	probably damaging	Het
Col16a1	G	A	4: 130,054,176	D230N	probably damaging	Het
Crhbp	C	A	13: 95,443,810	G87V	possibly damaging	Het
Cyp3a16	C	T	5: 145,452,834	M240I	probably benign	Het
Cyp4a14	A	T	4: 115,495,936	W60R	possibly damaging	Het
Fam47e	A	G	5: 92,585,290	Y304C	probably damaging	Het
Fgfbp1	A	T	5: 43,979,292	D219E	probably damaging	Het
Fgfr2	A	T	7: 130,185,272	Y485N	probably damaging	Het
Fhdc1	C	T	3: 84,453,533	V363M	probably damaging	Het
Foxb1	T	A	9: 69,760,155	E31V	probably damaging	Het
Galnt9	T	C	5: 110,544,739	V13A	possibly damaging	Het
Ghrl	T	C	6: 113,716,257	D77G	probably damaging	Het
Gm21731	A	G	13: 120,240,848	Y60C	probably damaging	Het
Gpr85	A	G	6: 13,835,978	V309A	probably benign	Het
Greb1	T	C	12: 16,681,471	Y1622C	probably damaging	Het
Greb1l	T	A	18: 10,547,447	M1555K	possibly damaging	Het
Grin2a	T	A	16: 9,669,823	N404Y	probably damaging	Het
Gtpbp1	A	C	15: 79,715,968	I399L	probably benign	Het
Hectd4	T	C	5: 121,322,690	S911P	possibly damaging	Het
Igkc	A	T	6: 70,726,536	K34*	probably null	Het
Igkv4-80	A	C	6: 69,016,665	S81A	probably benign	Het
Iqgap1	T	A	7: 80,765,317	I149F	probably damaging	Het
Lama1	C	T	17: 67,794,314	A1934V	probably benign	Het
Lrp1	C	A	10: 127,575,075	E1415*	probably null	Het
Macf1	A	C	4: 123,526,652	C270G	probably benign	Het
Marveld3	A	G	8: 109,948,311	V291A	probably benign	Het
Med23	T	C	10: 24,910,747	F917S	probably damaging	Het
Mfng	C	T	15: 78,764,388	R163H	probably benign	Het
Ncan	A	T	8: 70,109,954	D551E	probably benign	Het
Olfr1269	T	A	2: 90,118,777	T274S	probably damaging	Het
Olfr382	A	T	11: 73,517,172	I9N	possibly damaging	Het
Olfr649	T	C	7: 104,190,180	Y9C	possibly damaging	Het
Otx1	C	A	11: 21,997,037	A91S	probably damaging	Het
Pla2g12a	T	C	3: 129,878,818	W34R	probably damaging	Het
Plekha7	A	G	7: 116,158,128	F529S	probably damaging	Het
Ppl	T	A	16: 5,104,982	D215V	probably damaging	Het
Pramef20	A	T	4: 144,377,932	M1K	probably null	Het
Prkcd	T	A	14: 30,607,613	D124V	probably damaging	Het
Ptprc	C	A	1: 138,099,497	D538Y	probably benign	Het
Rasl10b	G	A	11: 83,412,679	V21M	probably damaging	Het
Rgsl1	T	A	1: 153,812,277	Y657F	probably benign	Het
Rrn3	T	C	16: 13,799,972	C360R	probably damaging	Het
Scarb1	T	C	5: 125,297,299	T257A	probably damaging	Het
Serpinb2	T	A	1: 107,515,489	M6K	probably benign	Het
Slco4a1	T	C	2: 180,472,056	Y429H	probably benign	Het
St13	G	C	15: 81,399,585	R4G	probably benign	Het
Taar3	T	A	10: 23,950,543	F329Y	probably damaging	Het
Tardbp	A	T	4: 148,618,651	N285K	probably benign	Het
Tnni2	A	T	7: 142,442,693	E4V	probably benign	Het
Tnpo2	A	T	8: 85,050,025	I454F	probably damaging	Het
Tpr	T	G	1: 150,432,565	H1690Q	probably benign	Het
Trav18	T	C	14: 53,831,120	S6P	probably benign	Het
Trf	T	C	9: 103,219,246	N25S	probably benign	Het
Vmn1r59	T	C	7: 5,454,116	N215S	probably benign	Het
Vmn2r2	T	C	3: 64,137,471	M1V	probably null	Het
Wdr64	T	C	1: 175,724,702		probably null	Het
Wdr73	T	C	7: 80,893,195	S222G	probably benign	Het

Other mutations in Prdm1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00657:Prdm1	APN	10	44441892	missense	probably damaging	1.00
IGL01331:Prdm1	APN	10	44441974	missense	possibly damaging	0.67
IGL02064:Prdm1	APN	10	44441342	missense	probably damaging	1.00
IGL02669:Prdm1	APN	10	44439884	missense	probably benign	0.28
IGL02944:Prdm1	APN	10	44441811	missense	probably benign
IGL03295:Prdm1	APN	10	44439870	missense	probably damaging	0.99
PIT4576001:Prdm1	UTSW	10	44458508	start codon destroyed	probably null	0.05
R0008:Prdm1	UTSW	10	44441679	missense	probably damaging	1.00
R0166:Prdm1	UTSW	10	44440091	missense	probably damaging	1.00
R0226:Prdm1	UTSW	10	44456696	missense	probably benign	0.03
R0284:Prdm1	UTSW	10	44456626	missense	probably damaging	1.00
R0398:Prdm1	UTSW	10	44439809	missense	probably damaging	1.00
R1200:Prdm1	UTSW	10	44450130	missense	probably damaging	1.00
R1405:Prdm1	UTSW	10	44439965	missense	probably damaging	1.00
R1405:Prdm1	UTSW	10	44439965	missense	probably damaging	1.00
R1438:Prdm1	UTSW	10	44442128	missense	probably benign	0.00
R1519:Prdm1	UTSW	10	44439986	nonsense	probably null
R1886:Prdm1	UTSW	10	44439758	missense	probably damaging	0.99
R2070:Prdm1	UTSW	10	44441412	missense	possibly damaging	0.82
R2508:Prdm1	UTSW	10	44446807	missense	probably benign	0.37
R3087:Prdm1	UTSW	10	44446827	missense	probably damaging	1.00
R3150:Prdm1	UTSW	10	44458492	splice site	probably null
R4165:Prdm1	UTSW	10	44441576	missense	probably benign	0.11
R4490:Prdm1	UTSW	10	44446907	nonsense	probably null
R4647:Prdm1	UTSW	10	44439690	missense	probably damaging	0.98
R4911:Prdm1	UTSW	10	44442052	missense	possibly damaging	0.90
R5153:Prdm1	UTSW	10	44450225	missense	possibly damaging	0.94
R5247:Prdm1	UTSW	10	44440102	missense	probably damaging	1.00
R5792:Prdm1	UTSW	10	44450228	missense	probably damaging	1.00
R6164:Prdm1	UTSW	10	44450195	missense	probably damaging	1.00
R6247:Prdm1	UTSW	10	44446786	splice site	probably null
R7196:Prdm1	UTSW	10	44456992	missense	probably benign	0.14
R7270:Prdm1	UTSW	10	44441570	missense	probably benign	0.07
R7384:Prdm1	UTSW	10	44458507	missense	probably benign	0.01
R7822:Prdm1	UTSW	10	44458482	missense	probably benign	0.01
R8809:Prdm1	UTSW	10	44439753	missense	probably benign
R8827:Prdm1	UTSW	10	44458480	missense	probably benign	0.00
R8932:Prdm1	UTSW	10	44441339	missense	probably damaging	1.00
R8958:Prdm1	UTSW	10	44440733	missense	probably damaging	1.00
R9009:Prdm1	UTSW	10	44447001	missense	probably benign	0.02
R9020:Prdm1	UTSW	10	44440040	missense	probably damaging	1.00
R9176:Prdm1	UTSW	10	44440127	missense	probably damaging	1.00
R9378:Prdm1	UTSW	10	44440154	missense	probably damaging	1.00
R9471:Prdm1	UTSW	10	44450178	missense	probably damaging	1.00
R9535:Prdm1	UTSW	10	44441612	missense	probably damaging	1.00
R9554:Prdm1	UTSW	10	44441246	missense	probably benign	0.01
Z1088:Prdm1	UTSW	10	44441925	missense	probably damaging	1.00
Z1176:Prdm1	UTSW	10	44446833	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TCAGATCCTCCAAAGGCAGC -3'
(R):5'- CATGAGCATTGTTAAGAGGCTTCTG -3'

Sequencing Primer
(F):5'- TCCAAAGGCAGCCCAGCAG -3'
(R):5'- CATTGTTAAGAGGCTTCTGGTCTC -3'

Posted On

2016-04-15