Mutagenetix > Incidental Mutation

Incidental Mutation 'R7988:Setd1a'

651592

Institutional Source

Beutler Lab

Gene Symbol

Setd1a

Ensembl Gene

ENSMUSG00000042308

Gene Name

SET domain containing 1A

Synonyms

KMT2F

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7988 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

127776670-127800122 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 127786194 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 691 (M691K)

Ref Sequence

ENSEMBL: ENSMUSP00000047672 (fasta)

Gene Model

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

AlphaFold

E9PYH6

Predicted Effect

probably benign
Transcript: ENSMUST00000047075
AA Change: M691K

PolyPhen 2 Score 0.024 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000047672
Gene: ENSMUSG00000042308
AA Change: M691K

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: ENSMUST00000047157
AA Change: M691K

PolyPhen 2 Score 0.024 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000037600
Gene: ENSMUSG00000042308
AA Change: M691K

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

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
AA Change: M148K

PolyPhen 2 Score 0.024 (Sensitivity: 0.95; Specificity: 0.81)

Meta Mutation Damage Score

0.0861

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

Validation Efficiency

100% (59/59)

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: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610030E20Rik	C	T	6: 72,347,652	T56M	probably damaging	Het
2010111I01Rik	A	G	13: 63,061,140	D357G	probably benign	Het
4932415D10Rik	T	C	10: 82,296,100	I359V	probably benign	Het
Adamtsl5	C	T	10: 80,345,538	S36N	probably benign	Het
Adgrf5	A	T	17: 43,439,813		probably benign	Het
Ago1	A	G	4: 126,460,417	F200S	probably damaging	Het
Akr1cl	T	C	1: 65,024,706	D108G	possibly damaging	Het
Arhgef3	A	T	14: 27,401,786	D468V	probably benign	Het
Aspn	T	C	13: 49,551,877	C72R	possibly damaging	Het
Baz2b	T	C	2: 59,962,141	T548A	possibly damaging	Het
Birc6	G	A	17: 74,599,373		probably null	Het
Btnl2	A	T	17: 34,358,275	T135S	possibly damaging	Het
Ccnl1	T	A	3: 65,957,861	I90F	possibly damaging	Het
Ccnt1	T	C	15: 98,565,143		probably null	Het
Cemip	C	A	7: 84,003,408		probably benign	Het
Cfap45	A	G	1: 172,529,934	D85G	probably damaging	Het
Cfap54	T	A	10: 92,902,079	D2319V	unknown	Het
Cma1	T	C	14: 55,944,532	M14V	possibly damaging	Het
Cmtm1	T	C	8: 104,310,142		probably benign	Het
Col27a1	A	G	4: 63,331,322	H1738R	unknown	Het
Colq	T	A	14: 31,553,837	D41V	probably damaging	Het
Cubn	T	C	2: 13,332,355	T2437A	probably benign	Het
Dnah14	A	G	1: 181,783,574	D3755G	probably damaging	Het
Eprs	A	G	1: 185,418,348	Y1349C	probably damaging	Het
Eps8	C	T	6: 137,528,571	R53Q	possibly damaging	Het
Fam196a	T	G	7: 134,917,698	K368Q	probably damaging	Het
Fbf1	T	C	11: 116,152,768	D405G	probably benign	Het
Fen1	C	T	19: 10,200,310	E257K	possibly damaging	Het
Gstm7	A	T	3: 107,926,955	M198K	possibly damaging	Het
Hook3	A	T	8: 26,073,647	S190T	probably benign	Het
Htra4	A	C	8: 25,030,510		probably null	Het
Ighv1-15	T	C	12: 114,657,496	I70V	probably benign	Het
Ikzf4	T	A	10: 128,634,455	N452Y	probably damaging	Het
Iqcf5	T	A	9: 106,515,821	N92K	possibly damaging	Het
Itk	A	G	11: 46,355,834	Y186H	probably damaging	Het
Klhdc10	T	C	6: 30,446,691	S282P	probably benign	Het
Klhl18	T	A	9: 110,476,509	E29V	possibly damaging	Het
Ky	T	C	9: 102,525,415	S140P	probably damaging	Het
Lmntd2	T	C	7: 141,213,637	E112G	unknown	Het
Lrrc36	C	A	8: 105,452,086	D304E	possibly damaging	Het
Macf1	A	T	4: 123,506,480	F674Y	probably damaging	Het
Notch1	C	T	2: 26,471,001	D1111N	probably benign	Het
Osbpl8	T	G	10: 111,272,080	N312K	possibly damaging	Het
Otogl	C	T	10: 107,895,776	C168Y	probably damaging	Het
Phldb2	T	G	16: 45,825,571	T171P	probably benign	Het
Ppef2	A	T	5: 92,238,982	F365L	probably benign	Het
Repin1	G	T	6: 48,597,345	E403*	probably null	Het
Ryr1	G	A	7: 29,096,171	T1105I	probably benign	Het
Sclt1	T	A	3: 41,663,454	*29L	probably null	Het
Scn11a	T	C	9: 119,765,437	K1297E	probably damaging	Het
Serpinb9c	T	A	13: 33,150,279	Y288F	probably benign	Het
Sftpc	T	C	14: 70,522,619	E66G	probably damaging	Het
Thnsl2	T	C	6: 71,141,319	T42A	probably benign	Het
Tram1	T	C	1: 13,569,975	D285G	probably benign	Het
Ttn	A	T	2: 76,736,240	I28103K	probably damaging	Het
Ttn	G	A	2: 76,845,030	P11137L	unknown	Het
Ttn	C	A	2: 76,896,759	V5821F	unknown	Het
Usp38	T	A	8: 81,014,316	M41L	probably benign	Het
Zcwpw1	T	G	5: 137,817,491	Y419D	possibly damaging	Het
Zfp407	G	A	18: 84,559,400	A1196V	possibly damaging	Het
Zfp446	T	A	7: 12,979,043	S103T	possibly damaging	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
R2159:Setd1a	UTSW	7	127785489	missense	possibly damaging	0.91
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
R8029:Setd1a	UTSW	7	127786214	missense	probably benign	0.08
R8079:Setd1a	UTSW	7	127785053	missense	unknown
R8171:Setd1a	UTSW	7	127791227	missense	unknown
R8175:Setd1a	UTSW	7	127796243	missense	unknown
R8286:Setd1a	UTSW	7	127786184	missense	possibly damaging	0.96
R8327:Setd1a	UTSW	7	127791497	missense	unknown
R8460:Setd1a	UTSW	7	127784120	missense	unknown
R8547:Setd1a	UTSW	7	127796504	unclassified	probably benign
R8699:Setd1a	UTSW	7	127786602	missense	possibly damaging	0.53
R8822:Setd1a	UTSW	7	127786160	missense	possibly damaging	0.86
R8968:Setd1a	UTSW	7	127786107	missense	possibly damaging	0.93
R9063:Setd1a	UTSW	7	127786386	missense	possibly damaging	0.91
R9178:Setd1a	UTSW	7	127786418	missense	possibly damaging	0.93
R9672:Setd1a	UTSW	7	127786065	missense	possibly damaging	0.96
R9700:Setd1a	UTSW	7	127786580	missense	possibly damaging	0.53
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
Z1176:Setd1a	UTSW	7	127799094	missense	unknown

Predicted Primers

PCR Primer
(F):5'- ATCTCTGATGATGACAGGGGTG -3'
(R):5'- GTGTGTACAGAGCATAGGGC -3'

Sequencing Primer
(F):5'- TGATGACAGGGGTGGCTCAC -3'
(R):5'- GCATAGGGCAAGCCATAGG -3'

Posted On

2020-09-15