Mutagenetix > Incidental Mutations

Incidental Mutation 'R4627:Prdm16'

348848

Institutional Source

Beutler Lab

Gene Symbol

Prdm16

Ensembl Gene

ENSMUSG00000039410

Gene Name

PR domain containing 16

Synonyms

Mel1, 5730557K01Rik, csp1, line 27

MMRRC Submission

041892-MU

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.804) question?

Stock #

R4627 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

154316125-154636873 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 154367240 bp

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Asparagine at position 170 (Y170N)

Ref Sequence

ENSEMBL: ENSMUSP00000117598 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030902] [ENSMUST00000070313] [ENSMUST00000097759] [ENSMUST00000105636] [ENSMUST00000105637] [ENSMUST00000105638] [ENSMUST00000124771]

Predicted Effect

probably damaging
Transcript: ENSMUST00000030902
AA Change: Y171N

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000030902
Gene: ENSMUSG00000039410
AA Change: Y171N

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 damaging
Transcript: ENSMUST00000070313
AA Change: Y172N

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000064546
Gene: ENSMUSG00000039410
AA Change: Y172N

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 damaging
Transcript: ENSMUST00000097759
AA Change: Y171N

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000095365
Gene: ENSMUSG00000039410
AA Change: Y171N

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 damaging
Transcript: ENSMUST00000105636
AA Change: Y172N

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

SMART Domains

Protein: ENSMUSP00000101261
Gene: ENSMUSG00000039410
AA Change: Y172N

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 damaging
Transcript: ENSMUST00000105637
AA Change: Y170N

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000101262
Gene: ENSMUSG00000039410
AA Change: Y170N

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 damaging
Transcript: ENSMUST00000105638
AA Change: Y171N

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000101263
Gene: ENSMUSG00000039410
AA Change: Y171N

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 damaging
Transcript: ENSMUST00000124771
AA Change: Y170N

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

SMART Domains

Protein: ENSMUSP00000117598
Gene: ENSMUSG00000039410
AA Change: Y170N

Domain	Start	End	E-Value	Type
low complexity region	44	57	N/A	INTRINSIC
low complexity region	74	83	N/A	INTRINSIC
SET	84	213	8.04e-4	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141164

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.3%
20x: 95.4%

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: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2010111I01Rik	T	C	13: 63,068,092	S393P	probably benign	Het
Adam6a	A	T	12: 113,544,949	D314V	probably benign	Het
Adamts18	C	T	8: 113,773,168	W371*	probably null	Het
Adamtsl2	T	A	2: 27,093,585	L331Q	probably damaging	Het
Akr1c13	G	T	13: 4,197,870	V214F	probably damaging	Het
Aldoart1	T	C	4: 72,852,443	T43A	probably benign	Het
Alkbh2	C	T	5: 114,124,226	E148K	probably damaging	Het
Ano7	T	C	1: 93,375,185	I15T	probably benign	Het
Aox3	A	T	1: 58,125,035	T155S	probably damaging	Het
Ap2a1	C	T	7: 44,904,419	V535M	probably damaging	Het
Apbb2	C	T	5: 66,400,076		probably null	Het
Astn1	C	A	1: 158,502,251	H225Q	possibly damaging	Het
Atm	A	G	9: 53,456,506	I2439T	possibly damaging	Het
Atp1b2	T	A	11: 69,601,334	I263F	probably damaging	Het
Ccdc184	A	T	15: 98,168,757	N148Y	probably benign	Het
Cdca7	TGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA	TGAAGAAGAAGAAGAAGAAGAAGAAGAAGA	2: 72,481,861		probably benign	Het
Cep192	C	G	18: 67,812,369	P180R	probably benign	Het
Cfap46	T	C	7: 139,657,281	Y571C	probably damaging	Het
Cfap46	A	T	7: 139,680,927	L85Q	probably damaging	Het
Chchd6	G	A	6: 89,384,660	L226F	probably damaging	Het
Cnot6l	A	G	5: 96,077,211	V541A	probably benign	Het
Cobl	T	C	11: 12,251,093	E1214G	probably damaging	Het
Cpsf2	G	A	12: 101,989,895	R319Q	probably benign	Het
Csdc2	T	C	15: 81,949,123	V107A	probably benign	Het
Csmd1	A	G	8: 16,697,917	W273R	probably benign	Het
Diexf	T	C	1: 193,107,695	T719A	probably benign	Het
Dnah2	T	A	11: 69,465,376	N2156I	probably damaging	Het
Dsp	A	G	13: 38,168,641	Y165C	probably benign	Het
Exoc1	T	C	5: 76,542,228	V205A	probably benign	Het
Fam98c	T	C	7: 29,155,268	T49A	possibly damaging	Het
Fbln2	G	T	6: 91,259,767	V755L	probably damaging	Het
Fhad1	A	T	4: 141,896,468	V1371D	possibly damaging	Het
Folh1	A	T	7: 86,773,252	M59K	probably benign	Het
Foxf2	A	T	13: 31,626,888	H270L	probably benign	Het
Gm14401	G	A	2: 177,086,316	R65H	probably benign	Het
Gpn1	C	A	5: 31,498,393	Y592*	probably null	Het
Hmcn1	T	G	1: 150,595,894	D4903A	probably benign	Het
Hnf1a	T	C	5: 114,955,871	R220G	probably damaging	Het
Hoxd10	G	A	2: 74,692,292	A105T	probably benign	Het
Kcnd3	C	T	3: 105,658,766	A421V	probably damaging	Het
Kidins220	C	T	12: 25,057,042	T1498I	possibly damaging	Het
Klhl2	G	T	8: 64,758,191	Y274*	probably null	Het
Lmbrd1	A	G	1: 24,705,999	Y140C	probably damaging	Het
Mapk8ip3	G	A	17: 24,903,293	T706I	probably benign	Het
Mast4	A	C	13: 103,334,021	S58A	possibly damaging	Het
Mcm6	T	C	1: 128,351,548	D167G	probably benign	Het
Mmachc	A	T	4: 116,703,471	S276T	probably damaging	Het
Nfat5	A	T	8: 107,369,276	Q1289L	probably damaging	Het
Nlrc4	G	T	17: 74,446,628	F253L	probably damaging	Het
Nr1i3	C	A	1: 171,216,445	A112E	probably benign	Het
Olfr1367	T	C	13: 21,347,464	F179L	probably damaging	Het
Olfr45	T	A	7: 140,691,378	S158T	probably benign	Het
Olfr455	T	A	6: 42,538,441	T194S	possibly damaging	Het
Olfr853	G	T	9: 19,537,673	Q86K	possibly damaging	Het
Orc5	G	T	5: 22,548,005	F10L	probably benign	Het
Pde10a	A	C	17: 8,981,652	D779A	probably damaging	Het
Pde4b	T	C	4: 102,601,605	L486S	probably damaging	Het
Pex2	A	T	3: 5,561,281	I156N	probably damaging	Het
Phtf2	C	T	5: 20,773,740	R63Q	probably damaging	Het
Prag1	A	G	8: 36,103,292	Y343C	probably damaging	Het
Prpf6	A	C	2: 181,601,474	K5T	probably damaging	Het
Ptpn1	A	G	2: 167,967,781	K103R	probably benign	Het
Ralgapa2	A	G	2: 146,361,453	S1159P	possibly damaging	Het
Rapgef3	G	T	15: 97,758,929	D318E	probably damaging	Het
Ripk4	A	T	16: 97,744,026	S474T	probably damaging	Het
Rmi1	A	G	13: 58,409,136	R400G	probably benign	Het
Sec16a	A	G	2: 26,429,393	V1491A	probably damaging	Het
Sec16a	C	T	2: 26,431,068		probably null	Het
Setd7	G	T	3: 51,542,665	N113K	probably damaging	Het
Shank2	C	T	7: 144,411,424	T1502M	probably damaging	Het
Skor1	A	T	9: 63,145,476	C376S	probably damaging	Het
Slc12a3	A	T	8: 94,329,384	L49F	probably benign	Het
Slc35d3	C	T	10: 19,849,331	V260M	probably damaging	Het
Slc46a1	T	A	11: 78,466,889	V256E	probably benign	Het
Slc6a1	T	C	6: 114,308,106	S127P	probably benign	Het
Syngr4	A	G	7: 45,887,028	L190P	probably damaging	Het
Tagap	G	A	17: 7,926,941		probably null	Het
Tamm41	A	T	6: 115,035,002	N89K	probably benign	Het
Tbc1d31	T	A	15: 57,967,912	M922K	probably benign	Het
Tbk1	T	C	10: 121,568,080	N254S	possibly damaging	Het
Tfec	A	G	6: 16,840,479	S140P	probably damaging	Het
Tnrc18	T	C	5: 142,740,128	E1802G	unknown	Het
Tom1l2	C	T	11: 60,242,707		probably null	Het
Tonsl	T	G	15: 76,637,224	K323Q	probably damaging	Het
Tsnaxip1	A	T	8: 105,841,407	E268D	probably damaging	Het
Ttf1	C	A	2: 29,065,160	H179N	possibly damaging	Het
Ttn	T	C	2: 76,726,173	S30163G	probably damaging	Het
Ube2c	A	G	2: 164,772,173	N143S	possibly damaging	Het
Ugt1a10	G	A	1: 88,218,390	R519Q	probably damaging	Het
Vmn2r9	T	C	5: 108,847,597	Y395C	probably damaging	Het
Vwa8	G	A	14: 79,103,697		probably null	Het
Zfp9	A	G	6: 118,464,976	Y242H	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
R2117:Prdm16	UTSW	4	154347925	missense	probably null	0.99
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
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
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'- CAGGTGTCAAATGGCTACCC -3'
(R):5'- TTAGACAACCTGCCATCCTG -3'

Sequencing Primer
(F):5'- GCAGGTGACCCATGACCTTATTAG -3'
(R):5'- AACCTGCCATCCTGCCTGAC -3'

Posted On

2015-10-08