Mutagenetix > Incidental Mutations

Incidental Mutation 'R2159:Setd1a'

235050

Institutional Source

Beutler Lab

Gene Symbol

Setd1a

Ensembl Gene

ENSMUSG00000042308

Gene Name

SET domain containing 1A

Synonyms

KMT2F

MMRRC Submission

040162-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R2159 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

127776670-127800122 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 127785489 bp

Zygosity

Heterozygous

Amino Acid Change

Arginine to Histidine at position 504 (R504H)

Ref Sequence

ENSEMBL: ENSMUSP00000037600 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047075] [ENSMUST00000047157] [ENSMUST00000126761] [ENSMUST00000144406] [ENSMUST00000154987]

Predicted Effect

possibly damaging
Transcript: ENSMUST00000047075
AA Change: R504H

PolyPhen 2 Score 0.906 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000047672
Gene: ENSMUSG00000042308
AA Change: R504H

Domain	Start	End	E-Value	Type
RRM	95	168	7.6e-6	SMART
low complexity region	209	242	N/A	INTRINSIC
low complexity region	278	295	N/A	INTRINSIC
low complexity region	315	357	N/A	INTRINSIC
low complexity region	427	487	N/A	INTRINSIC
Blast:SET	488	976	N/A	BLAST
low complexity region	977	1007	N/A	INTRINSIC
low complexity region	1015	1079	N/A	INTRINSIC
low complexity region	1087	1098	N/A	INTRINSIC
low complexity region	1122	1152	N/A	INTRINSIC
low complexity region	1157	1173	N/A	INTRINSIC
Blast:SET	1193	1310	2e-24	BLAST
low complexity region	1311	1368	N/A	INTRINSIC
low complexity region	1369	1396	N/A	INTRINSIC
N-SET	1428	1567	6.75e-64	SMART
SET	1577	1700	3.22e-35	SMART
PostSET	1700	1716	1.16e-4	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000047157
AA Change: R504H

PolyPhen 2 Score 0.906 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000037600
Gene: ENSMUSG00000042308
AA Change: R504H

Domain	Start	End	E-Value	Type
RRM	95	168	7.6e-6	SMART
low complexity region	209	242	N/A	INTRINSIC
low complexity region	278	295	N/A	INTRINSIC
low complexity region	315	357	N/A	INTRINSIC
low complexity region	427	487	N/A	INTRINSIC
Blast:SET	488	976	N/A	BLAST
low complexity region	977	1007	N/A	INTRINSIC
low complexity region	1015	1079	N/A	INTRINSIC
low complexity region	1087	1098	N/A	INTRINSIC
low complexity region	1122	1152	N/A	INTRINSIC
low complexity region	1157	1173	N/A	INTRINSIC
Blast:SET	1193	1310	2e-24	BLAST
low complexity region	1311	1368	N/A	INTRINSIC
low complexity region	1369	1396	N/A	INTRINSIC
N-SET	1428	1567	6.75e-64	SMART
SET	1577	1700	3.22e-35	SMART
PostSET	1700	1716	1.16e-4	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000126761

SMART Domains

Protein: ENSMUSP00000120666
Gene: ENSMUSG00000042308

Domain	Start	End	E-Value	Type
RRM	95	168	7.6e-6	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141439

Predicted Effect

probably benign
Transcript: ENSMUST00000144406

SMART Domains

Protein: ENSMUSP00000115248
Gene: ENSMUSG00000042308

Domain	Start	End	E-Value	Type
RRM	95	168	7.6e-6	SMART
low complexity region	209	242	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000154987

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.3%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a component of a histone methyltransferase (HMT) complex that produces mono-, di-, and trimethylated histone H3 at Lys4. Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to generally mark the transcription start sites of active genes. The protein contains SET domains, a RNA recognition motif domain and is a member of the class V-like SAM-binding methyltransferase superfamily. [provided by RefSeq, Dec 2016]
PHENOTYPE: Animals homozygous for this allele were dead by E7.5 [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam21	G	A	12: 81,560,467	P174S	probably benign	Het
Aida	C	T	1: 183,322,379	P185S	probably benign	Het
Alg11	T	G	8: 22,065,845	I374R	probably benign	Het
Ano9	T	C	7: 141,108,117	I229V	probably benign	Het
Apob	A	T	12: 8,010,081	L2821F	probably benign	Het
Atp10b	C	T	11: 43,151,853	T80I	possibly damaging	Het
BC024139	T	C	15: 76,121,488	H478R	probably damaging	Het
Btbd1	A	T	7: 81,801,056	D325E	possibly damaging	Het
Camk2a	G	A	18: 60,957,185	C199Y	probably damaging	Het
Casp3	A	G	8: 46,634,288	D90G	probably damaging	Het
Ccnt2	A	G	1: 127,775,154	H71R	probably benign	Het
Cdk2ap1	G	A	5: 124,348,604	R65*	probably null	Het
Cebpb	G	T	2: 167,689,253	A78S	probably benign	Het
Col5a3	A	G	9: 20,771,310	F1613L	unknown	Het
Cpd	T	C	11: 76,797,641	D935G	probably damaging	Het
Csmd3	CCTTTGCGCTT	CCTT	15: 47,741,236		probably null	Het
Cwc27	A	G	13: 104,804,329	I174T	probably damaging	Het
Cyp21a1	C	A	17: 34,802,404	R331L	probably benign	Het
Dnah5	A	G	15: 28,252,545	T795A	probably benign	Het
Eif2ak2	A	G	17: 78,874,018	V100A	possibly damaging	Het
Foxa3	A	G	7: 19,014,184	V339A	probably benign	Het
Gp2	T	C	7: 119,452,284	D236G	probably benign	Het
Gprc6a	CAAA	CA	10: 51,615,680		probably null	Het
Gzmd	T	A	14: 56,130,696	H102L	probably damaging	Het
Klk1b1	A	T	7: 43,970,433	I139F	probably damaging	Het
Lcmt2	G	A	2: 121,139,285	P439L	probably damaging	Het
Loxl4	C	T	19: 42,600,007	A570T	probably damaging	Het
Mga	T	A	2: 119,919,643	H674Q	probably damaging	Het
Mybpc3	A	T	2: 91,125,370	K583M	probably damaging	Het
Ncoa6	G	T	2: 155,407,713	P1224T	probably damaging	Het
Nostrin	A	G	2: 69,180,922		probably null	Het
Olfr1264	A	T	2: 90,021,538	V176E	probably damaging	Het
Olfr70	T	C	4: 43,697,110	H21R	probably benign	Het
Oxsr1	A	C	9: 119,304,814	D58E	possibly damaging	Het
Parm1	A	G	5: 91,613,064	Y265C	probably damaging	Het
Phf10	C	T	17: 14,952,664	E304K	probably damaging	Het
Prmt5	T	C	14: 54,515,338	T139A	probably benign	Het
Ptgir	A	G	7: 16,906,869	M29V	possibly damaging	Het
Ptp4a3	A	G	15: 73,752,016	T32A	probably benign	Het
Pwwp2b	A	T	7: 139,254,928	D95V	possibly damaging	Het
Rad51ap2	T	C	12: 11,457,751	L558S	possibly damaging	Het
Rapgef4	A	G	2: 72,174,881	D80G	probably damaging	Het
Sec24a	T	G	11: 51,712,350	H757P	probably damaging	Het
Sema4d	T	C	13: 51,720,535	N129D	probably damaging	Het
Serpini1	A	G	3: 75,623,944	T323A	probably benign	Het
Sftpb	T	C	6: 72,309,786	C226R	probably damaging	Het
Sp8	T	C	12: 118,848,706	S99P	possibly damaging	Het
Srgap3	A	G	6: 112,771,378	F438L	probably damaging	Het
Stim2	T	C	5: 54,109,814	Y365H	probably damaging	Het
Stk36	A	G	1: 74,634,737	Q1263R	probably benign	Het
Tectb	C	G	19: 55,180,999		probably benign	Het
Troap	G	T	15: 99,077,586	A184S	probably damaging	Het
Ttn	G	A	2: 76,899,327		probably benign	Het
Vmn2r108	C	A	17: 20,469,101	A531S	probably benign	Het
Vmn2r12	T	A	5: 109,091,474	I408F	probably benign	Het
Vmn2r8	T	A	5: 108,802,303	E226V	probably benign	Het
Vmo1	A	G	11: 70,513,782	F131S	probably benign	Het
Vwf	T	C	6: 125,626,341	F885L	probably damaging	Het
Wdpcp	A	T	11: 21,857,476	M618L	probably benign	Het
Wdr90	T	C	17: 25,851,741	E1072G	probably benign	Het

Other mutations in Setd1a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02508:Setd1a	APN	7	127797698	unclassified	probably benign
IGL02657:Setd1a	APN	7	127795825	unclassified	probably benign
IGL02792:Setd1a	APN	7	127791350	missense	unknown
IGL02876:Setd1a	APN	7	127778501	splice site	probably benign
IGL02967:Setd1a	APN	7	127785177	unclassified	probably benign
IGL03090:Setd1a	APN	7	127786500	missense	possibly damaging	0.83
IGL03238:Setd1a	APN	7	127785546	missense	possibly damaging	0.86
FR4449:Setd1a	UTSW	7	127785326	unclassified	probably benign
FR4548:Setd1a	UTSW	7	127785307	unclassified	probably benign
FR4548:Setd1a	UTSW	7	127785313	unclassified	probably benign
FR4589:Setd1a	UTSW	7	127785297	unclassified	probably benign
FR4737:Setd1a	UTSW	7	127785312	unclassified	probably benign
FR4976:Setd1a	UTSW	7	127785307	unclassified	probably benign
FR4976:Setd1a	UTSW	7	127785316	unclassified	probably benign
R0367:Setd1a	UTSW	7	127788186	splice site	probably benign
R0411:Setd1a	UTSW	7	127796051	unclassified	probably benign
R0416:Setd1a	UTSW	7	127785297	unclassified	probably benign
R0470:Setd1a	UTSW	7	127785057	unclassified	probably benign
R0645:Setd1a	UTSW	7	127787210	missense	probably damaging	0.96
R0667:Setd1a	UTSW	7	127786593	missense	probably damaging	0.99
R1251:Setd1a	UTSW	7	127797424	unclassified	probably benign
R1465:Setd1a	UTSW	7	127788340	unclassified	probably benign
R1465:Setd1a	UTSW	7	127788340	unclassified	probably benign
R1660:Setd1a	UTSW	7	127796669	unclassified	probably benign
R1730:Setd1a	UTSW	7	127785124	nonsense	probably null
R1760:Setd1a	UTSW	7	127785890	missense	possibly damaging	0.68
R1783:Setd1a	UTSW	7	127785124	nonsense	probably null
R2149:Setd1a	UTSW	7	127786518	missense	possibly damaging	0.75
R2303:Setd1a	UTSW	7	127799155	unclassified	probably benign
R2679:Setd1a	UTSW	7	127795724	unclassified	probably benign
R3428:Setd1a	UTSW	7	127785321	unclassified	probably benign
R4108:Setd1a	UTSW	7	127799202	unclassified	probably benign
R4227:Setd1a	UTSW	7	127796647	unclassified	probably benign
R4438:Setd1a	UTSW	7	127785731	missense	possibly damaging	0.83
R4730:Setd1a	UTSW	7	127797330	unclassified	probably benign
R4869:Setd1a	UTSW	7	127797604	unclassified	probably benign
R4892:Setd1a	UTSW	7	127778524	missense	probably damaging	0.99
R5152:Setd1a	UTSW	7	127784025	missense	probably benign
R5502:Setd1a	UTSW	7	127797248	critical splice donor site	probably null
R5527:Setd1a	UTSW	7	127785629	missense	probably damaging	0.99
R6189:Setd1a	UTSW	7	127778283	splice site	probably null
R6250:Setd1a	UTSW	7	127791299	missense	unknown
R7131:Setd1a	UTSW	7	127796418	small deletion	probably benign
RF001:Setd1a	UTSW	7	127785314	unclassified	probably benign
RF008:Setd1a	UTSW	7	127785314	unclassified	probably benign
RF011:Setd1a	UTSW	7	127785343	unclassified	probably benign
RF014:Setd1a	UTSW	7	127785346	unclassified	probably benign
RF030:Setd1a	UTSW	7	127785301	unclassified	probably benign
RF030:Setd1a	UTSW	7	127785311	unclassified	probably benign
RF031:Setd1a	UTSW	7	127785311	unclassified	probably benign
RF036:Setd1a	UTSW	7	127785300	unclassified	probably benign
RF041:Setd1a	UTSW	7	127785332	unclassified	probably benign
RF052:Setd1a	UTSW	7	127785357	unclassified	probably benign
RF055:Setd1a	UTSW	7	127785299	unclassified	probably benign
RF056:Setd1a	UTSW	7	127785303	unclassified	probably benign
RF056:Setd1a	UTSW	7	127785328	unclassified	probably benign
RF058:Setd1a	UTSW	7	127785318	unclassified	probably benign

Predicted Primers

PCR Primer
(F):5'- TATTTGGCCCCTGAGCCTAAC -3'
(R):5'- TCAAAATTAGCTGGTGCAGGAG -3'

Sequencing Primer
(F):5'- TGAGCCTAACCGATCCACTG -3'
(R):5'- GGAGGTGTACAGGGCCCATG -3'

Posted On

2014-10-01