Mutagenetix > Incidental Mutation

Incidental Mutation 'R5892:Prdm16'

457239

Institutional Source

Beutler Lab

Gene Symbol

Prdm16

Ensembl Gene

ENSMUSG00000039410

Gene Name

PR domain containing 16

Synonyms

Mel1, 5730557K01Rik, csp1, line 27

MMRRC Submission

044093-MU

Accession Numbers

Is this an essential gene?

Possibly essential (E-score: 0.735) question?

Stock #

R5892 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

154316125-154636873 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 154323259 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 1170 (D1170G)

Ref Sequence

ENSEMBL: ENSMUSP00000101261 (fasta)

Gene Model

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

AlphaFold

A2A935

Predicted Effect

probably benign
Transcript: ENSMUST00000030902
AA Change: D1169G

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000030902
Gene: ENSMUSG00000039410
AA Change: D1169G

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 benign
Transcript: ENSMUST00000070313
AA Change: D1171G

PolyPhen 2 Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000064546
Gene: ENSMUSG00000039410
AA Change: D1171G

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 benign
Transcript: ENSMUST00000097759
AA Change: D1170G

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000095365
Gene: ENSMUSG00000039410
AA Change: D1170G

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

possibly damaging
Transcript: ENSMUST00000105636
AA Change: D1170G

PolyPhen 2 Score 0.740 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000101261
Gene: ENSMUSG00000039410
AA Change: D1170G

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 benign
Transcript: ENSMUST00000105637
AA Change: D1168G

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000101262
Gene: ENSMUSG00000039410
AA Change: D1168G

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 benign
Transcript: ENSMUST00000105638
AA Change: D1170G

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000101263
Gene: ENSMUSG00000039410
AA Change: D1170G

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: ENSMUST00000141164

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145217

Meta Mutation Damage Score

0.0741

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.6%
20x: 92.6%

Validation Efficiency

98% (56/57)

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: 49 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930524J08Rik	G	T	5: 99,979,265		probably benign	Het
Abcb11	C	T	2: 69,261,500	A893T	probably damaging	Het
Adtrp	A	T	13: 41,828,206	N30K	probably benign	Het
Alms1	T	A	6: 85,620,903	S904T	probably damaging	Het
Cep170	T	A	1: 176,755,387		probably null	Het
Cntnap3	A	G	13: 64,799,180	V145A	probably damaging	Het
Dclre1a	T	C	19: 56,547,140	E4G	probably benign	Het
Depdc1a	G	C	3: 159,526,669	A686P	probably damaging	Het
Dnah7b	T	C	1: 46,337,593		probably null	Het
Enox1	A	G	14: 77,486,017		probably benign	Het
Fam107b	A	G	2: 3,778,564	E268G	probably damaging	Het
Fer1l6	A	G	15: 58,564,068	S437G	probably benign	Het
Flnb	C	A	14: 7,907,183	T1252K	probably damaging	Het
Fubp1	A	G	3: 152,218,314		probably benign	Het
Gm20402	G	A	3: 52,268,949	A50T	probably benign	Het
Gpr137b	T	C	13: 13,359,406	Y355C		Het
Gzmk	C	T	13: 113,173,922		probably null	Het
Ino80	A	T	2: 119,439,547		probably benign	Het
Ints8	T	C	4: 11,223,813	T677A	probably damaging	Het
Kat6a	A	G	8: 22,938,289	E1220G	probably damaging	Het
Lrfn5	A	G	12: 61,843,418	T498A	probably damaging	Het
Lrp2	T	A	2: 69,442,776	T4043S	probably benign	Het
Malrd1	A	G	2: 15,614,267	N314S	probably benign	Het
Mfsd1	A	G	3: 67,589,829		probably null	Het
Muc1	C	T	3: 89,230,993	P381S	probably benign	Het
Myh2	A	T	11: 67,185,176	K730*	probably null	Het
Nat3	T	A	8: 67,547,938	N156K	probably benign	Het
Nelfe	T	C	17: 34,854,669		probably benign	Het
Nlrp1a	A	T	11: 71,099,645	L927Q	probably damaging	Het
P4ha2	A	G	11: 54,120,188	Y343C	probably damaging	Het
Pclo	A	T	5: 14,521,171	Q190L	probably damaging	Het
Pde8a	A	G	7: 81,295,691	N183S	probably damaging	Het
Plekha2	C	T	8: 25,052,365	V278I	probably benign	Het
Plekha6	G	C	1: 133,272,307	R208P	possibly damaging	Het
Plxnb1	T	C	9: 109,111,707	L1550P	probably damaging	Het
Ppox	C	T	1: 171,277,461	V385I	probably damaging	Het
Prmt5	A	T	14: 54,509,911	S470T	probably damaging	Het
Robo2	T	A	16: 73,895,780		probably benign	Het
Siglecg	G	A	7: 43,412,204		probably benign	Het
Slc30a5	T	C	13: 100,813,302	N367S	probably damaging	Het
Tex29	C	T	8: 11,854,288		probably benign	Het
Tmem117	T	A	15: 94,638,139	V18E	probably damaging	Het
Tmtc2	C	T	10: 105,413,505	M122I	probably benign	Het
Tpr	T	A	1: 150,407,400	N287K	probably benign	Het
Unc93b1	A	T	19: 3,943,632	D358V	probably damaging	Het
Vrk2	A	T	11: 26,534,372		probably benign	Het
Wdr24	A	T	17: 25,827,986	Q671L	probably benign	Het
Zfp110	C	T	7: 12,848,478	T351I	probably benign	Het
Zfp963	T	C	8: 69,743,377	D142G	probably benign	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
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
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'- AACTCTGGCTAGCATCACCC -3'
(R):5'- TTACAGGCCTGAGATCCAAGAC -3'

Sequencing Primer
(F):5'- CTAAGCCTAGTGCCAAAGCCTTG -3'
(R):5'- TGGACAGCAACCCACCGTG -3'

Posted On

2017-02-15