Mutagenetix > Incidental Mutation

Incidental Mutation 'R5561:Prdm4'

501197

Institutional Source

Beutler Lab

Gene Symbol

Prdm4

Ensembl Gene

ENSMUSG00000035529

Gene Name

PR domain containing 4

Synonyms

SC-1, SC1, 1700031E19Rik, 2810470D21Rik

MMRRC Submission

043118-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5561 (G1)

Quality Score

217

Status

Not validated

Chromosome

Chromosomal Location

85727828-85752958 bp(-) (GRCm39)

Type of Mutation

makesense

DNA Base Change (assembly)

TCTCCTCCT to TCTCCT at 85728987 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000151931 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000001836] [ENSMUST00000037646] [ENSMUST00000219370] [ENSMUST00000220032]

AlphaFold

Q80V63

Predicted Effect

probably benign
Transcript: ENSMUST00000001836

SMART Domains

Protein: ENSMUSP00000001836
Gene: ENSMUSG00000001785

Domain	Start	End	E-Value	Type
low complexity region	45	61	N/A	INTRINSIC
Blast:WD40	168	220	4e-27	BLAST
WD40	244	284	4.51e-7	SMART
WD40	287	327	3.37e-6	SMART
WD40	331	370	4.42e1	SMART
WD40	373	413	6.38e-7	SMART
Blast:WD40	418	458	3e-23	BLAST

Predicted Effect

probably null
Transcript: ENSMUST00000037646

SMART Domains

Protein: ENSMUSP00000041942
Gene: ENSMUSG00000035529

Domain	Start	End	E-Value	Type
low complexity region	14	28	N/A	INTRINSIC
low complexity region	33	44	N/A	INTRINSIC
low complexity region	51	69	N/A	INTRINSIC
low complexity region	339	353	N/A	INTRINSIC
PDB:3DB5\|B	386	543	2e-98	PDB
Blast:SET	408	538	5e-82	BLAST
ZnF_C2H2	548	569	7.77e1	SMART
low complexity region	575	588	N/A	INTRINSIC
ZnF_C2H2	593	615	3.78e-1	SMART
ZnF_C2H2	621	643	2.27e-4	SMART
ZnF_C2H2	649	671	8.02e-5	SMART
ZnF_C2H2	677	699	3.63e-3	SMART
ZnF_C2H2	705	727	3.11e-2	SMART
ZnF_C2H2	733	753	1.81e1	SMART
low complexity region	759	780	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000218743

Predicted Effect

probably benign
Transcript: ENSMUST00000219370

Predicted Effect

probably null
Transcript: ENSMUST00000220032

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 97.9%
20x: 93.4%

Validation Efficiency

MGI Phenotype

FUNCTION: This gene encodes a member of the PR/SET family of zinc finger proteins. This protein has been shown to bind DNA in a sequence-specific manner and has been implicated in neural stem cell proliferation and differentiation. Pseudogenes have been identified on chromosomes 14 and X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]
PHENOTYPE: Mice homozygous for alleles lacking the zinc finger domain or PR/SET domain exhibit no abnormal phenotype. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A630095N17Rik	T	C	1: 75,197,181 (GRCm39)		probably benign	Het
Acyp2	C	T	11: 30,456,354 (GRCm39)	E98K	possibly damaging	Het
Adgrv1	A	G	13: 81,624,683 (GRCm39)	L3762P	probably damaging	Het
Amn1	G	A	6: 149,086,522 (GRCm39)	R4W	probably damaging	Het
Atxn1	G	T	13: 45,720,347 (GRCm39)	T516N	possibly damaging	Het
Atxn7	A	T	14: 14,089,260 (GRCm38)	T259S	probably benign	Het
Bsn	C	G	9: 107,982,710 (GRCm39)	R3681P	unknown	Het
C8b	T	C	4: 104,641,645 (GRCm39)	Y194H	possibly damaging	Het
Ccdc110	T	G	8: 46,393,646 (GRCm39)	S119R	probably benign	Het
Ccdc202	C	A	14: 96,119,807 (GRCm39)	A188E	probably benign	Het
Ceacam20	A	T	7: 19,704,318 (GRCm39)	Q123L	possibly damaging	Het
Clip3	A	G	7: 29,998,274 (GRCm39)	D240G	possibly damaging	Het
Col24a1	T	C	3: 145,004,588 (GRCm39)	F22S	probably benign	Het
Dlg5	T	A	14: 24,227,860 (GRCm39)	M354L	probably benign	Het
Dnajb12	GC	G	10: 59,728,574 (GRCm39)		probably null	Het
Dnase1l3	A	G	14: 7,967,847 (GRCm38)	V282A	probably damaging	Het
Dnhd1	G	A	7: 105,364,028 (GRCm39)	G4127S	probably damaging	Het
Eed	G	A	7: 89,617,001 (GRCm39)	R165W	probably damaging	Het
Ephb2	C	T	4: 136,388,717 (GRCm39)	V627M	probably damaging	Het
Fancc	T	C	13: 63,465,201 (GRCm39)	E502G	possibly damaging	Het
Fbf1	T	C	11: 116,048,646 (GRCm39)	D105G	probably damaging	Het
Fer	T	A	17: 64,344,580 (GRCm39)	Y246*	probably null	Het
Fer1l6	A	G	15: 58,532,674 (GRCm39)	K1792E	probably damaging	Het
Foxi2	A	G	7: 135,013,376 (GRCm39)	D202G	probably damaging	Het
Gm11595	G	A	11: 99,663,381 (GRCm39)	R100C	unknown	Het
H2-DMb2	G	T	17: 34,364,445 (GRCm39)		probably null	Het
Helq	G	T	5: 100,934,916 (GRCm39)	D491E	probably benign	Het
Hgsnat	A	G	8: 26,436,362 (GRCm39)	V564A	possibly damaging	Het
Hjurp	GT	GTT	1: 88,194,246 (GRCm39)		probably null	Het
Hs3st5	T	A	10: 36,709,425 (GRCm39)	V320D	probably damaging	Het
Ifit1bl1	A	T	19: 34,571,197 (GRCm39)	L420*	probably null	Het
Ift80	T	G	3: 68,875,196 (GRCm39)	N178T	probably benign	Het
Ing4	C	T	6: 125,024,023 (GRCm39)	T89I	possibly damaging	Het
Lcp1	G	A	14: 75,449,948 (GRCm39)	D386N	probably benign	Het
Mdc1	T	A	17: 36,159,438 (GRCm39)	I606K	probably benign	Het
Mllt10	T	A	2: 18,114,656 (GRCm39)	M120K	probably damaging	Het
Morc1	G	T	16: 48,269,711 (GRCm39)	L89F	probably benign	Het
Mroh2a	GCCC	GC	1: 88,159,979 (GRCm39)		probably null	Het
Nav3	C	A	10: 109,552,413 (GRCm39)	D1810Y	probably damaging	Het
Obscn	G	A	11: 58,926,919 (GRCm39)	T5532M	probably damaging	Het
Opn3	C	T	1: 175,493,153 (GRCm39)	R137H	probably damaging	Het
Or12j2	C	T	7: 139,916,065 (GRCm39)	Q97*	probably null	Het
Or2d36	A	G	7: 106,747,297 (GRCm39)	N258S	probably benign	Het
Palld	G	A	8: 61,969,619 (GRCm39)	A993V	probably damaging	Het
Ppp1r12c	A	T	7: 4,489,355 (GRCm39)		probably null	Het
Rapgef2	A	T	3: 78,995,950 (GRCm39)		probably null	Het
Ring1	T	C	17: 34,240,432 (GRCm39)	E382G	possibly damaging	Het
Rpl22l1	T	A	3: 28,860,969 (GRCm39)	N61K	probably benign	Het
Rpp14	A	G	14: 8,090,558 (GRCm38)		probably null	Het
Rusc2	C	T	4: 43,415,932 (GRCm39)	Q413*	probably null	Het
Slco3a1	A	G	7: 73,968,247 (GRCm39)	I491T	possibly damaging	Het
Smtnl1	C	T	2: 84,648,739 (GRCm39)	V172I	probably benign	Het
Spats2l	T	A	1: 57,939,780 (GRCm39)		probably null	Het
Spire1	T	A	18: 67,639,716 (GRCm39)	N266Y	probably damaging	Het
Stox2	T	C	8: 47,646,041 (GRCm39)	H473R	probably damaging	Het
Syne2	C	T	12: 76,141,232 (GRCm39)	R121*	probably null	Het
Synrg	G	A	11: 83,893,066 (GRCm39)		probably null	Het
Tm9sf1	C	T	14: 55,875,554 (GRCm39)	V397M	probably damaging	Het
Trabd	T	C	15: 88,966,187 (GRCm39)	M48T	probably benign	Het
Ttn	T	A	2: 76,537,577 (GRCm39)	I26457F	possibly damaging	Het
Uggt2	C	T	14: 119,278,939 (GRCm39)	R856Q	probably benign	Het
Ugt1a5	T	A	1: 88,094,039 (GRCm39)	M89K	probably benign	Het
Vmn2r53	A	T	7: 12,335,347 (GRCm39)	S104R	probably damaging	Het
Zdhhc12	A	T	2: 29,982,496 (GRCm39)	L53Q	probably null	Het

Other mutations in Prdm4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01864:Prdm4	APN	10	85,729,100 (GRCm39)	missense	probably benign	0.08
IGL02514:Prdm4	APN	10	85,743,781 (GRCm39)	missense	probably damaging	0.99
IGL02576:Prdm4	APN	10	85,736,801 (GRCm39)	missense	possibly damaging	0.86
IGL02674:Prdm4	APN	10	85,729,263 (GRCm39)	missense	probably damaging	0.99
IGL03002:Prdm4	APN	10	85,729,016 (GRCm39)	missense	probably benign	0.08
IGL03153:Prdm4	APN	10	85,743,860 (GRCm39)	missense	probably benign
IGL03278:Prdm4	APN	10	85,743,622 (GRCm39)	missense	probably damaging	0.99
IGL03338:Prdm4	APN	10	85,743,685 (GRCm39)	missense	possibly damaging	0.90
R0020:Prdm4	UTSW	10	85,743,487 (GRCm39)	missense	probably benign
R0133:Prdm4	UTSW	10	85,746,085 (GRCm39)	critical splice donor site	probably null
R0366:Prdm4	UTSW	10	85,743,868 (GRCm39)	missense	probably damaging	1.00
R0633:Prdm4	UTSW	10	85,743,767 (GRCm39)	missense	probably damaging	1.00
R1132:Prdm4	UTSW	10	85,735,145 (GRCm39)	missense	probably damaging	1.00
R1460:Prdm4	UTSW	10	85,743,686 (GRCm39)	missense	probably benign	0.28
R1477:Prdm4	UTSW	10	85,740,129 (GRCm39)	missense	probably benign	0.00
R1680:Prdm4	UTSW	10	85,735,087 (GRCm39)	missense	possibly damaging	0.96
R1772:Prdm4	UTSW	10	85,729,256 (GRCm39)	missense	probably damaging	0.99
R1983:Prdm4	UTSW	10	85,743,817 (GRCm39)	missense	probably damaging	1.00
R2136:Prdm4	UTSW	10	85,729,215 (GRCm39)	nonsense	probably null
R3426:Prdm4	UTSW	10	85,746,153 (GRCm39)	missense	probably damaging	1.00
R3723:Prdm4	UTSW	10	85,735,145 (GRCm39)	missense	probably damaging	1.00
R4490:Prdm4	UTSW	10	85,736,763 (GRCm39)	missense	probably damaging	1.00
R4750:Prdm4	UTSW	10	85,735,085 (GRCm39)	missense	probably damaging	1.00
R5601:Prdm4	UTSW	10	85,728,987 (GRCm39)	makesense	probably null
R5602:Prdm4	UTSW	10	85,728,987 (GRCm39)	makesense	probably null
R5604:Prdm4	UTSW	10	85,728,987 (GRCm39)	makesense	probably null
R5972:Prdm4	UTSW	10	85,743,365 (GRCm39)	missense	probably damaging	1.00
R6272:Prdm4	UTSW	10	85,743,694 (GRCm39)	missense	possibly damaging	0.82
R6300:Prdm4	UTSW	10	85,746,085 (GRCm39)	critical splice donor site	probably null
R6457:Prdm4	UTSW	10	85,743,896 (GRCm39)	missense	probably damaging	1.00
R6605:Prdm4	UTSW	10	85,740,002 (GRCm39)	missense	probably benign	0.00
R6642:Prdm4	UTSW	10	85,743,682 (GRCm39)	missense	probably benign	0.00
R7663:Prdm4	UTSW	10	85,735,145 (GRCm39)	missense	probably damaging	1.00
R9064:Prdm4	UTSW	10	85,737,678 (GRCm39)	missense	probably damaging	0.98
R9071:Prdm4	UTSW	10	85,729,076 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- AAAGGGCACTTTGACTCAAGC -3'
(R):5'- CCTGAAGACCTGCAAAGAGC -3'

Sequencing Primer
(F):5'- CAGATAGTAAAAGTTGGCCCTCTC -3'
(R):5'- GACCTGCAAAGAGCCCAGC -3'

Posted On

2017-12-01