Mutagenetix > Incidental Mutation

Incidental Mutation 'R2117:Prdm16'

231047

Institutional Source

Beutler Lab

Gene Symbol

Prdm16

Ensembl Gene

ENSMUSG00000039410

Gene Name

PR domain containing 16

Synonyms

Mel1, 5730557K01Rik, csp1, line 27

MMRRC Submission

040121-MU

Accession Numbers

Is this an essential gene?

Possibly essential (E-score: 0.699) question?

Stock #

R2117 (G1)

Quality Score

212

Status

Not validated

Chromosome

Chromosomal Location

154316125-154636873 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 154347925 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Cysteine at position 296 (S296C)

Ref Sequence

ENSEMBL: ENSMUSP00000101263 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030902] [ENSMUST00000070313] [ENSMUST00000097759] [ENSMUST00000105636] [ENSMUST00000105637] [ENSMUST00000105638] [ENSMUST00000181143]

AlphaFold

A2A935

Predicted Effect

probably null
Transcript: ENSMUST00000030902
AA Change: S296C

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000030902
Gene: ENSMUSG00000039410
AA Change: S296C

Domain	Start	End	E-Value	Type
low complexity region	44	57	N/A	INTRINSIC
low complexity region	74	83	N/A	INTRINSIC
SET	84	217	8.75e-5	SMART
ZnF_C2H2	230	250	2.82e1	SMART
low complexity region	260	274	N/A	INTRINSIC
ZnF_C2H2	282	304	1.04e-3	SMART
ZnF_C2H2	310	332	1.6e-4	SMART
ZnF_C2H2	338	361	3.95e-4	SMART
ZnF_C2H2	367	389	1.95e-3	SMART
ZnF_C2H2	395	417	8.22e-2	SMART
ZnF_C2H2	424	451	9.96e0	SMART
low complexity region	496	517	N/A	INTRINSIC
low complexity region	520	540	N/A	INTRINSIC
low complexity region	610	641	N/A	INTRINSIC
ZnF_C2H2	951	973	5.29e-5	SMART
ZnF_C2H2	979	1002	1.6e-4	SMART
ZnF_C2H2	1008	1030	7.26e-3	SMART
low complexity region	1116	1132	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000070313
AA Change: S297C

PolyPhen 2 Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000064546
Gene: ENSMUSG00000039410
AA Change: S297C

Domain	Start	End	E-Value	Type
low complexity region	44	57	N/A	INTRINSIC
low complexity region	74	83	N/A	INTRINSIC
SET	84	218	8.75e-5	SMART
ZnF_C2H2	231	251	2.82e1	SMART
low complexity region	261	275	N/A	INTRINSIC
ZnF_C2H2	283	305	1.04e-3	SMART
ZnF_C2H2	311	333	1.6e-4	SMART
ZnF_C2H2	339	362	3.95e-4	SMART
ZnF_C2H2	368	390	1.95e-3	SMART
ZnF_C2H2	396	418	8.22e-2	SMART
ZnF_C2H2	425	452	9.96e0	SMART
low complexity region	497	518	N/A	INTRINSIC
low complexity region	521	541	N/A	INTRINSIC
low complexity region	611	642	N/A	INTRINSIC
ZnF_C2H2	953	975	5.29e-5	SMART
ZnF_C2H2	981	1004	1.6e-4	SMART
ZnF_C2H2	1010	1032	7.26e-3	SMART
low complexity region	1118	1134	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000097759
AA Change: S296C

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000095365
Gene: ENSMUSG00000039410
AA Change: S296C

Domain	Start	End	E-Value	Type
low complexity region	44	57	N/A	INTRINSIC
low complexity region	74	83	N/A	INTRINSIC
SET	84	217	8.75e-5	SMART
ZnF_C2H2	230	250	2.82e1	SMART
low complexity region	260	274	N/A	INTRINSIC
ZnF_C2H2	282	304	1.04e-3	SMART
ZnF_C2H2	310	332	1.6e-4	SMART
ZnF_C2H2	338	361	3.95e-4	SMART
ZnF_C2H2	367	389	1.95e-3	SMART
ZnF_C2H2	395	417	8.22e-2	SMART
ZnF_C2H2	424	451	9.96e0	SMART
low complexity region	496	517	N/A	INTRINSIC
low complexity region	520	540	N/A	INTRINSIC
low complexity region	610	641	N/A	INTRINSIC
ZnF_C2H2	952	974	5.29e-5	SMART
ZnF_C2H2	980	1003	1.6e-4	SMART
ZnF_C2H2	1009	1031	7.26e-3	SMART
low complexity region	1117	1133	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000105636
AA Change: S297C

PolyPhen 2 Score 0.951 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000101261
Gene: ENSMUSG00000039410
AA Change: S297C

Domain	Start	End	E-Value	Type
low complexity region	44	57	N/A	INTRINSIC
low complexity region	74	83	N/A	INTRINSIC
SET	84	218	8.75e-5	SMART
ZnF_C2H2	231	251	2.82e1	SMART
low complexity region	261	275	N/A	INTRINSIC
ZnF_C2H2	283	305	1.04e-3	SMART
ZnF_C2H2	311	333	1.6e-4	SMART
ZnF_C2H2	339	362	3.95e-4	SMART
ZnF_C2H2	368	390	1.95e-3	SMART
ZnF_C2H2	396	418	8.22e-2	SMART
ZnF_C2H2	425	452	9.96e0	SMART
low complexity region	497	518	N/A	INTRINSIC
low complexity region	521	541	N/A	INTRINSIC
low complexity region	611	642	N/A	INTRINSIC
ZnF_C2H2	952	974	5.29e-5	SMART
ZnF_C2H2	980	1003	1.6e-4	SMART
ZnF_C2H2	1009	1031	7.26e-3	SMART
low complexity region	1117	1133	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000105637
AA Change: S295C

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000101262
Gene: ENSMUSG00000039410
AA Change: S295C

Domain	Start	End	E-Value	Type
low complexity region	44	57	N/A	INTRINSIC
low complexity region	74	83	N/A	INTRINSIC
SET	84	216	8.75e-5	SMART
ZnF_C2H2	229	249	2.82e1	SMART
low complexity region	259	273	N/A	INTRINSIC
ZnF_C2H2	281	303	1.04e-3	SMART
ZnF_C2H2	309	331	1.6e-4	SMART
ZnF_C2H2	337	360	3.95e-4	SMART
ZnF_C2H2	366	388	1.95e-3	SMART
ZnF_C2H2	394	416	8.22e-2	SMART
ZnF_C2H2	423	450	9.96e0	SMART
low complexity region	495	516	N/A	INTRINSIC
low complexity region	519	539	N/A	INTRINSIC
low complexity region	609	640	N/A	INTRINSIC
ZnF_C2H2	950	972	5.29e-5	SMART
ZnF_C2H2	978	1001	1.6e-4	SMART
ZnF_C2H2	1007	1029	7.26e-3	SMART
low complexity region	1115	1131	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000105638
AA Change: S296C

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000101263
Gene: ENSMUSG00000039410
AA Change: S296C

Domain	Start	End	E-Value	Type
low complexity region	44	57	N/A	INTRINSIC
low complexity region	74	83	N/A	INTRINSIC
SET	84	217	8.75e-5	SMART
ZnF_C2H2	230	250	2.82e1	SMART
low complexity region	260	274	N/A	INTRINSIC
ZnF_C2H2	282	304	1.04e-3	SMART
ZnF_C2H2	310	332	1.6e-4	SMART
ZnF_C2H2	338	361	3.95e-4	SMART
ZnF_C2H2	367	389	1.95e-3	SMART
ZnF_C2H2	395	417	8.22e-2	SMART
ZnF_C2H2	424	451	9.96e0	SMART
low complexity region	496	517	N/A	INTRINSIC
low complexity region	520	540	N/A	INTRINSIC
low complexity region	610	641	N/A	INTRINSIC
ZnF_C2H2	952	974	5.29e-5	SMART
ZnF_C2H2	980	1003	1.6e-4	SMART
ZnF_C2H2	1009	1031	7.26e-3	SMART
low complexity region	1117	1133	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131762

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141164

Predicted Effect

probably benign
Transcript: ENSMUST00000181143

SMART Domains

Protein: ENSMUSP00000138001
Gene: ENSMUSG00000097871

Domain	Start	End	E-Value	Type
low complexity region	17	30	N/A	INTRINSIC

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.2%
20x: 95.0%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The reciprocal translocation t(1;3)(p36;q21) occurs in a subset of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). This gene is located near the 1p36.3 breakpoint and has been shown to be specifically expressed in the t(1:3)(p36,q21)-positive MDS/AML. The protein encoded by this gene is a zinc finger transcription factor and contains an N-terminal PR domain. The translocation results in the overexpression of a truncated version of this protein that lacks the PR domain, which may play an important role in the pathogenesis of MDS and AML. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mutant mice exhibit a cleft secondary palate, whitening of brown adipose tissue in older or fed a high-fat diet, and impaired adaptive thermogenesis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 101 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrv1	A	T	13: 81,492,537	C3357S	probably benign	Het
Ago1	T	A	4: 126,463,857		probably null	Het
Akap10	A	T	11: 61,890,303	D562E	possibly damaging	Het
Akr1b7	G	A	6: 34,418,994	A144T	possibly damaging	Het
Ankle1	A	G	8: 71,407,918	T340A	probably benign	Het
Arf5	C	T	6: 28,424,784	Q71*	probably null	Het
Arl15	C	T	13: 113,967,660	S111F	probably damaging	Het
Asph	G	A	4: 9,517,671	Q468*	probably null	Het
Bcam	G	T	7: 19,758,427	A581E	possibly damaging	Het
Blvra	G	T	2: 127,086,069	E80*	probably null	Het
Casc1	C	T	6: 145,205,241		probably null	Het
Ccr6	T	C	17: 8,256,082	F40L	possibly damaging	Het
Cfap161	A	T	7: 83,775,976	N302K	possibly damaging	Het
Ckmt2	T	A	13: 91,855,845	I345F	probably benign	Het
Cpsf6	A	G	10: 117,366,120		probably benign	Het
Ctnna1	A	G	18: 35,152,625	N8S	possibly damaging	Het
Cyp2d11	A	G	15: 82,391,753	L209P	probably damaging	Het
Dab2	T	C	15: 6,435,615	V628A	probably damaging	Het
Dcstamp	C	T	15: 39,755,175	Q327*	probably null	Het
Defb38	A	T	8: 19,023,467	Y63*	probably null	Het
Dlg5	A	T	14: 24,177,758	L365*	probably null	Het
Dnmt3l	C	A	10: 78,063,296	L110I	probably damaging	Het
Exoc3l2	G	T	7: 19,494,982	L108F	possibly damaging	Het
Exoc4	T	A	6: 33,347,825	N351K	possibly damaging	Het
Fam83h	C	A	15: 76,004,733	E252*	probably null	Het
Fancm	A	G	12: 65,077,174	D202G	probably damaging	Het
Fat1	T	A	8: 45,037,463	V3804E	probably benign	Het
Fbxw28	T	C	9: 109,330,917	T190A	probably benign	Het
Fer1l4	T	C	2: 156,039,118	T843A	probably benign	Het
Fnip1	A	T	11: 54,500,624	H461L	probably damaging	Het
Gcn1l1	A	T	5: 115,598,825	M1276L	probably benign	Het
Gemin4	A	G	11: 76,211,001	V978A	possibly damaging	Het
Gm7247	A	T	14: 51,365,335	I43F	probably damaging	Het
Gm853	C	A	4: 130,215,363	V295L	possibly damaging	Het
Gm9978	C	T	10: 78,486,897		noncoding transcript	Het
Gpr4	T	C	7: 19,223,145	S331P	probably damaging	Het
Hspa1a	T	A	17: 34,970,479	N483Y	probably damaging	Het
Ift74	A	G	4: 94,627,259	T138A	probably benign	Het
Ints14	T	G	9: 64,979,795	L336R	probably damaging	Het
Irak1	G	T	X: 74,022,612	P197Q	possibly damaging	Het
Kif4	A	G	X: 100,665,717	S315G	probably benign	Het
L3mbtl1	T	A	2: 162,960,070		probably null	Het
Lamb3	A	G	1: 193,334,181	R657G	probably benign	Het
Lrp2	A	C	2: 69,483,385	V2334G	probably benign	Het
Lrwd1	T	A	5: 136,130,478	Y431F	probably damaging	Het
Map3k21	A	T	8: 125,924,042	H261L	probably benign	Het
Meis1	G	T	11: 18,881,679	P453Q	probably damaging	Het
Mettl16	G	T	11: 74,802,929	M255I	probably benign	Het
Mllt10	A	G	2: 18,162,569	N435S	probably benign	Het
Mpp5	T	C	12: 78,809,922	F180L	possibly damaging	Het
Mta2	T	C	19: 8,943,516	I27T	probably damaging	Het
Nav2	A	G	7: 49,464,580	I771V	probably benign	Het
Nisch	A	T	14: 31,177,285		probably benign	Het
Npc1	G	A	18: 12,196,556	P990L	probably damaging	Het
Nrxn1	A	T	17: 90,704,277	I308K	probably damaging	Het
Olfr1378	A	T	11: 50,969,320	I101F	probably damaging	Het
Olfr1402	C	A	3: 97,410,449	C244F	probably damaging	Het
Olfr183	T	C	16: 59,000,420	L245P	possibly damaging	Het
Otogl	T	C	10: 107,858,918	D823G	probably benign	Het
P2rx7	A	G	5: 122,681,266	T584A	probably benign	Het
Pank1	T	A	19: 34,841,086	I18F	probably damaging	Het
Pgap3	A	G	11: 98,391,107	L126P	probably damaging	Het
Phka1	C	T	X: 102,610,201	R290H	probably damaging	Het
Pkd2	G	A	5: 104,483,176	E489K	probably damaging	Het
Prex2	T	A	1: 11,186,713	N1216K	probably damaging	Het
Prmt7	A	G	8: 106,227,298	T124A	probably damaging	Het
Ptpra	G	T	2: 130,539,735	R372L	probably damaging	Het
Ptpro	T	A	6: 137,443,594	V1007D	probably damaging	Het
Rap2b	G	T	3: 61,365,091	G12V	probably damaging	Het
Rapgef5	T	A	12: 117,714,064		probably null	Het
Rassf4	A	G	6: 116,645,127	F168S	possibly damaging	Het
Rtf1	T	A	2: 119,705,518	H184Q	probably benign	Het
Sacs	A	G	14: 61,213,771	K4422R	probably benign	Het
Sec11c	A	T	18: 65,800,649	T9S	probably benign	Het
Sema3d	C	T	5: 12,563,273	T439I	probably benign	Het
Sephs1	A	G	2: 4,899,540	N243S	probably benign	Het
Setd2	TTGGGA	T	9: 110,604,144		probably null	Het
Setx	A	G	2: 29,130,301	D100G	probably benign	Het
Slc22a7	C	A	17: 46,433,972	V383L	possibly damaging	Het
Slc25a40	T	C	5: 8,430,417	C56R	probably damaging	Het
Stk38l	T	A	6: 146,768,846	L229I	probably damaging	Het
Sult2a5	T	C	7: 13,625,434	S112P	probably damaging	Het
Syt4	A	G	18: 31,440,467	Y332H	probably damaging	Het
Tcof1	T	C	18: 60,832,785	E415G	possibly damaging	Het
Tenm2	A	G	11: 36,024,854	L1951P	probably damaging	Het
Tlr9	A	G	9: 106,225,337	N609S	probably damaging	Het
Tmem120a	A	T	5: 135,736,123	S266T	possibly damaging	Het
Tmem132b	A	G	5: 125,622,551	E92G	probably damaging	Het
Tmem8	C	T	17: 26,117,884	L259F	possibly damaging	Het
Tnfrsf18	T	A	4: 156,028,516	V196E	probably damaging	Het
Trpc1	A	T	9: 95,717,584	L474H	probably damaging	Het
Trpm6	T	C	19: 18,829,952	V1020A	probably damaging	Het
Usp20	T	A	2: 31,016,305	C562S	probably damaging	Het
Usp47	T	A	7: 112,067,236		probably null	Het
Vgll1	A	C	X: 57,092,430	K53T	probably damaging	Het
Vmn1r26	T	C	6: 58,008,350	N285D	possibly damaging	Het
Zfp445	T	A	9: 122,853,437	K480*	probably null	Het
Zfp786	A	G	6: 47,826,997	V37A	probably damaging	Het
Zfp821	A	G	8: 109,721,219	E64G	probably damaging	Het
Zfp994	T	A	17: 22,200,981	D329V	probably damaging	Het
Zkscan8	T	C	13: 21,520,318	S484G	probably damaging	Het

Other mutations in Prdm16

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00987:Prdm16	APN	4	154341969	missense	possibly damaging	0.89
IGL01517:Prdm16	APN	4	154328425	missense	probably damaging	1.00
IGL01810:Prdm16	APN	4	154347927	missense	probably benign	0.10
IGL02260:Prdm16	APN	4	154328287	missense	probably benign	0.00
IGL02623:Prdm16	APN	4	154340877	missense	probably damaging	0.98
IGL02744:Prdm16	APN	4	154345453	missense	probably damaging	1.00
R0126:Prdm16	UTSW	4	154328838	splice site	probably benign
R0345:Prdm16	UTSW	4	154341111	missense	probably benign	0.09
R0365:Prdm16	UTSW	4	154342056	missense	probably damaging	1.00
R0440:Prdm16	UTSW	4	154476627	splice site	probably benign
R0899:Prdm16	UTSW	4	154528909	missense	probably damaging	1.00
R1127:Prdm16	UTSW	4	154528799	missense	probably damaging	1.00
R1546:Prdm16	UTSW	4	154528660	missense	possibly damaging	0.94
R1803:Prdm16	UTSW	4	154335261	missense	probably damaging	1.00
R3814:Prdm16	UTSW	4	154328293	missense	probably damaging	1.00
R4348:Prdm16	UTSW	4	154476667	missense	probably benign	0.00
R4458:Prdm16	UTSW	4	154322308	missense	probably benign
R4557:Prdm16	UTSW	4	154528827	missense	probably benign	0.01
R4581:Prdm16	UTSW	4	154323353	missense	probably damaging	1.00
R4584:Prdm16	UTSW	4	154337683	missense	probably damaging	1.00
R4627:Prdm16	UTSW	4	154367240	missense	probably damaging	1.00
R4926:Prdm16	UTSW	4	154341552	missense	possibly damaging	0.74
R5055:Prdm16	UTSW	4	154335262	missense	possibly damaging	0.48
R5152:Prdm16	UTSW	4	154346102	missense	probably damaging	0.99
R5257:Prdm16	UTSW	4	154367214	missense	possibly damaging	0.89
R5258:Prdm16	UTSW	4	154367214	missense	possibly damaging	0.89
R5368:Prdm16	UTSW	4	154345391	missense	probably damaging	1.00
R5464:Prdm16	UTSW	4	154346144	critical splice acceptor site	probably null
R5640:Prdm16	UTSW	4	154341910	missense	probably benign
R5744:Prdm16	UTSW	4	154528704	missense	probably damaging	1.00
R5892:Prdm16	UTSW	4	154323259	missense	possibly damaging	0.74
R5938:Prdm16	UTSW	4	154347954	missense	probably damaging	0.99
R6380:Prdm16	UTSW	4	154341367	missense	probably benign	0.00
R6784:Prdm16	UTSW	4	154323307	missense	probably damaging	1.00
R7097:Prdm16	UTSW	4	154345468	missense	probably damaging	1.00
R7181:Prdm16	UTSW	4	154528637	missense	probably damaging	1.00
R7197:Prdm16	UTSW	4	154341510	missense	probably damaging	1.00
R7273:Prdm16	UTSW	4	154345453	missense	probably damaging	1.00
R7379:Prdm16	UTSW	4	154528859	missense	probably damaging	1.00
R7641:Prdm16	UTSW	4	154345444	missense	probably damaging	1.00
R7704:Prdm16	UTSW	4	154341490	missense	probably damaging	1.00
R7751:Prdm16	UTSW	4	154328299	missense	probably damaging	1.00
R8048:Prdm16	UTSW	4	154320882	missense	probably damaging	1.00
R8225:Prdm16	UTSW	4	154355245	critical splice donor site	probably null
R8503:Prdm16	UTSW	4	154341552	missense	probably benign	0.04
R8683:Prdm16	UTSW	4	154528704	missense	probably damaging	1.00
R8880:Prdm16	UTSW	4	154528913	missense	probably damaging	1.00
R9257:Prdm16	UTSW	4	154337698	missense	probably damaging	1.00
R9259:Prdm16	UTSW	4	154346068	missense	possibly damaging	0.69
RF008:Prdm16	UTSW	4	154341995	missense	probably damaging	1.00
X0010:Prdm16	UTSW	4	154323377	missense	probably damaging	1.00
Z1176:Prdm16	UTSW	4	154341786	missense	probably damaging	0.97

Predicted Primers

PCR Primer
(F):5'- AGCGGACCAGGACCTTTATG -3'
(R):5'- ACATTCCGCTGTGATGAGTG -3'

Sequencing Primer
(F):5'- CACATGGTTCCCAGTTCA -3'
(R):5'- TGATGAGCTCTTCCAGTGCAG -3'

Posted On

2014-09-18