Mutagenetix > Incidental Mutation

Incidental Mutation 'R9378:Prdm1'

709796

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

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9378 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

44313173-44404497 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 44316150 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Tyrosine at position 662 (C662Y)

Ref Sequence

ENSEMBL: ENSMUSP00000101129 (fasta)

Gene Model

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

AlphaFold

Q60636

Predicted Effect

probably damaging
Transcript: ENSMUST00000039174
AA Change: C695Y

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

SMART Domains

Protein: ENSMUSP00000039248
Gene: ENSMUSG00000038151
AA Change: C695Y

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 damaging
Transcript: ENSMUST00000105490
AA Change: C662Y

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

SMART Domains

Protein: ENSMUSP00000101129
Gene: ENSMUSG00000038151
AA Change: C662Y

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 damaging
Transcript: ENSMUST00000218369
AA Change: C677Y

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

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: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2210408I21Rik	A	G	13: 77,471,735 (GRCm39)	K1047E	possibly damaging	Het
Aadacl2fm1	A	G	3: 59,839,110 (GRCm39)	T11A	possibly damaging	Het
Abca14	A	T	7: 119,807,191 (GRCm39)	Y79F	possibly damaging	Het
Abca2	T	A	2: 25,329,094 (GRCm39)	M978K	probably benign	Het
Adamts3	A	T	5: 89,848,269 (GRCm39)	C684*	probably null	Het
Adnp2	T	C	18: 80,172,637 (GRCm39)	T591A	probably benign	Het
Aff4	A	T	11: 53,263,306 (GRCm39)	T109S	probably damaging	Het
Agmo	A	G	12: 37,293,720 (GRCm39)	I48V	probably benign	Het
Appl1	G	A	14: 26,649,784 (GRCm39)	R581*	probably null	Het
Armc9	A	T	1: 86,189,766 (GRCm39)	M714L	probably benign	Het
Atp6v0d2	T	A	4: 19,922,377 (GRCm39)	T41S	probably benign	Het
Bin1	A	T	18: 32,552,921 (GRCm39)	Q182L	probably damaging	Het
Bmp10	A	G	6: 87,410,684 (GRCm39)	D159G	probably benign	Het
Bsn	G	A	9: 107,984,854 (GRCm39)	P295S	possibly damaging	Het
Cbx6	A	G	15: 79,712,606 (GRCm39)	S274P	probably damaging	Het
Cdc20b	A	G	13: 113,192,631 (GRCm39)	K108R	probably benign	Het
Ces1d	T	A	8: 93,912,724 (GRCm39)	N238I	probably damaging	Het
Col7a1	C	T	9: 108,787,708 (GRCm39)	Q663*	probably null	Het
Cpsf3	T	C	12: 21,358,039 (GRCm39)	I517T	possibly damaging	Het
Cyp2a5	C	A	7: 26,539,879 (GRCm39)	T309N	probably damaging	Het
Cyp2d40	A	G	15: 82,645,802 (GRCm39)	F68L	possibly damaging	Het
Cyp7b1	A	T	3: 18,150,837 (GRCm39)	W301R	probably damaging	Het
Dnah6	T	A	6: 73,189,513 (GRCm39)	N45I	probably benign	Het
Dnah7a	A	T	1: 53,621,776 (GRCm39)	H1116Q	probably benign	Het
Dntt	A	G	19: 41,027,356 (GRCm39)	N141S	probably benign	Het
Fbxl13	T	C	5: 21,790,201 (GRCm39)	N281D	probably damaging	Het
Frem2	A	T	3: 53,559,410 (GRCm39)	L1699H	probably damaging	Het
Gabrr3	T	C	16: 59,282,037 (GRCm39)	V464A	possibly damaging	Het
Gdap1	T	A	1: 17,227,353 (GRCm39)	I160N	probably damaging	Het
Hnrnpll	C	A	17: 80,369,291 (GRCm39)	R44L	unknown	Het
Hsp90ab1	T	C	17: 45,881,680 (GRCm39)	E187G	probably damaging	Het
Ighm	T	A	12: 113,386,210 (GRCm39)	T47S		Het
Itgb7	A	C	15: 102,135,831 (GRCm39)		probably null	Het
Kif16b	A	T	2: 142,461,738 (GRCm39)	C1293*	probably null	Het
Klf11	C	T	12: 24,705,043 (GRCm39)	R166C	probably benign	Het
Lca5l	T	A	16: 95,977,212 (GRCm39)	Q198L	probably damaging	Het
Lnx2	A	T	5: 146,961,180 (GRCm39)	M584K	probably benign	Het
Lpp	A	T	16: 24,540,737 (GRCm39)	M1L	probably benign	Het
Lrig3	A	G	10: 125,832,953 (GRCm39)	T276A	probably damaging	Het
Ltbp2	G	A	12: 84,837,864 (GRCm39)	P1192L	probably benign	Het
Megf8	A	T	7: 25,039,840 (GRCm39)		probably null	Het
Myh1	A	C	11: 67,093,259 (GRCm39)	T117P	probably damaging	Het
Neb	C	A	2: 52,134,113 (GRCm39)	R3290L	possibly damaging	Het
Neb	A	C	2: 52,137,304 (GRCm39)	V220G		Het
Nktr	A	T	9: 121,577,264 (GRCm39)	K444I	probably damaging	Het
Nol11	A	T	11: 107,064,505 (GRCm39)	M483K	probably benign	Het
Npy1r	C	A	8: 67,156,861 (GRCm39)	P94T	probably damaging	Het
Nsmaf	T	C	4: 6,440,940 (GRCm39)	T37A	probably benign	Het
Or10ad1b	A	G	15: 98,124,920 (GRCm39)	L204P	possibly damaging	Het
Or2y3	G	A	17: 38,393,056 (GRCm39)	A271V	possibly damaging	Het
Or4c119	T	C	2: 88,987,399 (GRCm39)	N40S	probably damaging	Het
Or51v8	A	T	7: 103,319,389 (GRCm39)	M283K	probably damaging	Het
Or5w14	C	A	2: 87,541,423 (GRCm39)	V276F	possibly damaging	Het
Or8a1b	A	G	9: 37,623,473 (GRCm39)	I34T	probably damaging	Het
Or8b37	G	A	9: 37,958,775 (GRCm39)	V86M	possibly damaging	Het
Palld	C	T	8: 61,969,691 (GRCm39)	R1211H	unknown	Het
Pcdha3	A	G	18: 37,080,284 (GRCm39)	D342G	probably damaging	Het
Pclo	G	A	5: 14,815,877 (GRCm39)	V1266I		Het
Pcnx4	T	C	12: 72,602,664 (GRCm39)	Y309H	probably damaging	Het
Pde8a	C	T	7: 80,982,619 (GRCm39)	T746I	probably damaging	Het
Pdzrn3	T	G	6: 101,127,772 (GRCm39)	K965Q	probably damaging	Het
Phldb1	G	A	9: 44,615,425 (GRCm39)	A225V	probably benign	Het
Pierce1	TCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCGGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTC	TCTCTGGGGCAGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTCTGGGGCGGGCTTAGCCTTGGGCTCCCCCGGCTCCGGCTCCTC	2: 28,356,122 (GRCm39)		probably benign	Het
Plat	A	G	8: 23,265,599 (GRCm39)	Y214C	probably damaging	Het
Plppr1	T	A	4: 49,325,627 (GRCm39)	C274*	probably null	Het
Poglut1	A	G	16: 38,347,133 (GRCm39)	F345L	possibly damaging	Het
Ppara	A	T	15: 85,661,837 (GRCm39)	E26V	possibly damaging	Het
Ppcdc	A	T	9: 57,327,571 (GRCm39)	W79R	probably damaging	Het
Sgms2	G	A	3: 131,136,011 (GRCm39)		probably benign	Het
Slc31a1	T	A	4: 62,306,843 (GRCm39)	M133K	probably damaging	Het
Smg1	G	A	7: 117,777,998 (GRCm39)	Q1309*	probably null	Het
Sos1	T	C	17: 80,761,239 (GRCm39)	I152M	probably damaging	Het
Stk4	A	T	2: 163,952,136 (GRCm39)		probably benign	Het
Syne1	T	G	10: 5,200,954 (GRCm39)	N3538T	probably damaging	Het
Tbc1d16	A	G	11: 119,099,666 (GRCm39)	F236S	probably damaging	Het
Tgs1	T	A	4: 3,595,475 (GRCm39)	M548K	probably benign	Het
Twf1	G	A	15: 94,483,336 (GRCm39)	T124I	probably damaging	Het
Tyro3	G	A	2: 119,642,648 (GRCm39)	G611R	probably damaging	Het
Unc13b	T	A	4: 43,173,282 (GRCm39)	I1370K	unknown	Het
Usp40	A	G	1: 87,885,032 (GRCm39)	W939R	probably damaging	Het
Vamp8	A	T	6: 72,362,554 (GRCm39)	V82E	probably damaging	Het
Vmn2r17	A	G	5: 109,575,732 (GRCm39)	H201R	possibly damaging	Het
Whrn	T	C	4: 63,350,079 (GRCm39)	H546R	probably benign	Het
Yeats2	T	C	16: 20,033,228 (GRCm39)	V1036A	probably benign	Het
Zfp352	T	G	4: 90,112,575 (GRCm39)	N238K	probably benign	Het
Zfp36l3	TCCAGGGGCGAGGGCAGCCCCAGGAGCAAGGGCCGCCCTAGGAATGAGGGCCGCCCCAGG	TCCAGG	X: 52,776,521 (GRCm39)		probably benign	Het
Zfp462	T	A	4: 55,011,510 (GRCm39)	S1159T	probably benign	Het
Zscan4-ps1	A	T	7: 10,800,192 (GRCm39)	H232Q	probably benign	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
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
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'- TCAGATCCTCCAAAGGCAGC -3'
(R):5'- CATGAGCATTGTTAAGAGGCTTCTG -3'

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

Posted On

2022-04-18