Mutagenetix > Incidental Mutation

Incidental Mutation 'R3428:Setd1a'

267956

Institutional Source

Beutler Lab

Gene Symbol

Setd1a

Ensembl Gene

ENSMUSG00000042308

Gene Name

SET domain containing 1A

Synonyms

KMT2F

MMRRC Submission

040646-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R3428 (G1)

Quality Score

197

Status

Validated

Chromosome

Chromosomal Location

127376561-127399294 bp(+) (GRCm39)

Type of Mutation

unclassified

DNA Base Change (assembly)

G to T at 127384493 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000145647 (fasta)

Gene Model

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

AlphaFold

E9PYH6

Predicted Effect

unknown
Transcript: ENSMUST00000047075
AA Change: G448V

SMART Domains

Protein: ENSMUSP00000047672
Gene: ENSMUSG00000042308
AA Change: G448V

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

unknown
Transcript: ENSMUST00000047157
AA Change: G448V

SMART Domains

Protein: ENSMUSP00000037600
Gene: ENSMUSG00000042308
AA Change: G448V

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

Meta Mutation Damage Score

0.0624

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.9%

Validation Efficiency

100% (34/34)

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: 32 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam18	C	A	8: 25,157,620 (GRCm39)	C110F	probably damaging	Het
Adamts14	C	T	10: 61,060,153 (GRCm39)	E452K	probably benign	Het
Adrb3	T	C	8: 27,718,209 (GRCm39)	D80G	probably damaging	Het
Alg5	T	A	3: 54,643,006 (GRCm39)	M1K	probably null	Het
Ap1g1	A	G	8: 110,570,080 (GRCm39)	E398G	probably damaging	Het
Arhgap17	A	T	7: 122,922,854 (GRCm39)	L85Q	probably damaging	Het
Bbs9	T	A	9: 22,479,183 (GRCm39)		probably benign	Het
BC034090	T	C	1: 155,117,244 (GRCm39)	I291M	probably benign	Het
Bicd1	T	C	6: 149,414,400 (GRCm39)	L371P	probably damaging	Het
Cand2	A	C	6: 115,766,668 (GRCm39)	R424S	probably benign	Het
Eng	G	T	2: 32,547,545 (GRCm39)	V29F	probably damaging	Het
Gm5828	T	A	1: 16,838,838 (GRCm39)		noncoding transcript	Het
Hspg2	T	C	4: 137,282,601 (GRCm39)	L3447P	probably damaging	Het
Igtp	G	A	11: 58,097,419 (GRCm39)	V197I	probably damaging	Het
Kmt2a	T	A	9: 44,759,416 (GRCm39)	N844I	probably benign	Het
Lyzl4	T	C	9: 121,413,195 (GRCm39)	I78V	probably null	Het
Mtg2	A	G	2: 179,726,065 (GRCm39)	H225R	possibly damaging	Het
Or10a5	G	A	7: 106,635,923 (GRCm39)	R187K	probably benign	Het
Pfpl	T	A	19: 12,407,677 (GRCm39)	S643T	probably benign	Het
Prelid1	T	G	13: 55,470,007 (GRCm39)	V2G	probably benign	Het
Psma2	A	T	13: 14,791,362 (GRCm39)	K2N	probably benign	Het
Sec24d	C	T	3: 123,137,572 (GRCm39)		probably benign	Het
Slc20a1	A	T	2: 129,042,202 (GRCm39)	N149I	probably benign	Het
Slc22a5	A	G	11: 53,760,152 (GRCm39)	V388A	probably benign	Het
Tmem181a	T	A	17: 6,346,061 (GRCm39)	L185H	probably damaging	Het
Tns2	C	T	15: 102,017,369 (GRCm39)	R281C	probably damaging	Het
Trav6-7-dv9	A	G	14: 53,947,788 (GRCm39)	T97A	probably benign	Het
Trpv3	A	T	11: 73,176,767 (GRCm39)	Y382F	probably damaging	Het
Ubr2	T	C	17: 47,279,365 (GRCm39)	Y681C	probably damaging	Het
Unc80	G	A	1: 66,678,464 (GRCm39)	V2082I	probably benign	Het
Vmn2r125	A	G	4: 156,702,436 (GRCm39)	D74G	probably benign	Het
Yipf2	T	C	9: 21,500,941 (GRCm39)		probably benign	Het

Other mutations in Setd1a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02508:Setd1a	APN	7	127,396,870 (GRCm39)	unclassified	probably benign
IGL02657:Setd1a	APN	7	127,394,997 (GRCm39)	unclassified	probably benign
IGL02792:Setd1a	APN	7	127,390,522 (GRCm39)	missense	unknown
IGL02876:Setd1a	APN	7	127,377,673 (GRCm39)	splice site	probably benign
IGL02967:Setd1a	APN	7	127,384,349 (GRCm39)	unclassified	probably benign
IGL03090:Setd1a	APN	7	127,385,672 (GRCm39)	missense	possibly damaging	0.83
IGL03238:Setd1a	APN	7	127,384,718 (GRCm39)	missense	possibly damaging	0.86
FR4449:Setd1a	UTSW	7	127,384,498 (GRCm39)	unclassified	probably benign
FR4548:Setd1a	UTSW	7	127,384,485 (GRCm39)	unclassified	probably benign
FR4548:Setd1a	UTSW	7	127,384,479 (GRCm39)	unclassified	probably benign
FR4589:Setd1a	UTSW	7	127,384,469 (GRCm39)	unclassified	probably benign
FR4737:Setd1a	UTSW	7	127,384,484 (GRCm39)	unclassified	probably benign
FR4976:Setd1a	UTSW	7	127,384,488 (GRCm39)	unclassified	probably benign
FR4976:Setd1a	UTSW	7	127,384,479 (GRCm39)	unclassified	probably benign
R0367:Setd1a	UTSW	7	127,387,358 (GRCm39)	splice site	probably benign
R0411:Setd1a	UTSW	7	127,395,223 (GRCm39)	unclassified	probably benign
R0416:Setd1a	UTSW	7	127,384,469 (GRCm39)	unclassified	probably benign
R0470:Setd1a	UTSW	7	127,384,229 (GRCm39)	unclassified	probably benign
R0645:Setd1a	UTSW	7	127,386,382 (GRCm39)	missense	probably damaging	0.96
R0667:Setd1a	UTSW	7	127,385,765 (GRCm39)	missense	probably damaging	0.99
R1251:Setd1a	UTSW	7	127,396,596 (GRCm39)	unclassified	probably benign
R1465:Setd1a	UTSW	7	127,387,512 (GRCm39)	unclassified	probably benign
R1465:Setd1a	UTSW	7	127,387,512 (GRCm39)	unclassified	probably benign
R1660:Setd1a	UTSW	7	127,395,841 (GRCm39)	unclassified	probably benign
R1730:Setd1a	UTSW	7	127,384,296 (GRCm39)	nonsense	probably null
R1760:Setd1a	UTSW	7	127,385,062 (GRCm39)	missense	possibly damaging	0.68
R1783:Setd1a	UTSW	7	127,384,296 (GRCm39)	nonsense	probably null
R2149:Setd1a	UTSW	7	127,385,690 (GRCm39)	missense	possibly damaging	0.75
R2159:Setd1a	UTSW	7	127,384,661 (GRCm39)	missense	possibly damaging	0.91
R2303:Setd1a	UTSW	7	127,398,327 (GRCm39)	unclassified	probably benign
R2679:Setd1a	UTSW	7	127,394,896 (GRCm39)	unclassified	probably benign
R4108:Setd1a	UTSW	7	127,398,374 (GRCm39)	unclassified	probably benign
R4227:Setd1a	UTSW	7	127,395,819 (GRCm39)	unclassified	probably benign
R4438:Setd1a	UTSW	7	127,384,903 (GRCm39)	missense	possibly damaging	0.83
R4730:Setd1a	UTSW	7	127,396,502 (GRCm39)	unclassified	probably benign
R4869:Setd1a	UTSW	7	127,396,776 (GRCm39)	unclassified	probably benign
R4892:Setd1a	UTSW	7	127,377,696 (GRCm39)	missense	probably damaging	0.99
R5152:Setd1a	UTSW	7	127,383,197 (GRCm39)	missense	probably benign
R5502:Setd1a	UTSW	7	127,396,420 (GRCm39)	critical splice donor site	probably null
R5527:Setd1a	UTSW	7	127,384,801 (GRCm39)	missense	probably damaging	0.99
R6189:Setd1a	UTSW	7	127,377,455 (GRCm39)	splice site	probably null
R6250:Setd1a	UTSW	7	127,390,471 (GRCm39)	missense	unknown
R7131:Setd1a	UTSW	7	127,395,590 (GRCm39)	small deletion	probably benign
R7988:Setd1a	UTSW	7	127,385,366 (GRCm39)	missense	probably benign	0.02
R8029:Setd1a	UTSW	7	127,385,386 (GRCm39)	missense	probably benign	0.08
R8079:Setd1a	UTSW	7	127,384,225 (GRCm39)	missense	unknown
R8171:Setd1a	UTSW	7	127,390,399 (GRCm39)	missense	unknown
R8175:Setd1a	UTSW	7	127,395,415 (GRCm39)	missense	unknown
R8286:Setd1a	UTSW	7	127,385,356 (GRCm39)	missense	possibly damaging	0.96
R8327:Setd1a	UTSW	7	127,390,669 (GRCm39)	missense	unknown
R8460:Setd1a	UTSW	7	127,383,292 (GRCm39)	missense	unknown
R8547:Setd1a	UTSW	7	127,395,676 (GRCm39)	unclassified	probably benign
R8699:Setd1a	UTSW	7	127,385,774 (GRCm39)	missense	possibly damaging	0.53
R8822:Setd1a	UTSW	7	127,385,332 (GRCm39)	missense	possibly damaging	0.86
R8968:Setd1a	UTSW	7	127,385,279 (GRCm39)	missense	possibly damaging	0.93
R9063:Setd1a	UTSW	7	127,385,558 (GRCm39)	missense	possibly damaging	0.91
R9178:Setd1a	UTSW	7	127,385,590 (GRCm39)	missense	possibly damaging	0.93
R9672:Setd1a	UTSW	7	127,385,237 (GRCm39)	missense	possibly damaging	0.96
R9700:Setd1a	UTSW	7	127,385,752 (GRCm39)	missense	possibly damaging	0.53
RF001:Setd1a	UTSW	7	127,384,486 (GRCm39)	unclassified	probably benign
RF008:Setd1a	UTSW	7	127,384,486 (GRCm39)	unclassified	probably benign
RF011:Setd1a	UTSW	7	127,384,515 (GRCm39)	unclassified	probably benign
RF014:Setd1a	UTSW	7	127,384,518 (GRCm39)	unclassified	probably benign
RF030:Setd1a	UTSW	7	127,384,483 (GRCm39)	unclassified	probably benign
RF030:Setd1a	UTSW	7	127,384,473 (GRCm39)	unclassified	probably benign
RF031:Setd1a	UTSW	7	127,384,483 (GRCm39)	unclassified	probably benign
RF036:Setd1a	UTSW	7	127,384,472 (GRCm39)	unclassified	probably benign
RF041:Setd1a	UTSW	7	127,384,504 (GRCm39)	unclassified	probably benign
RF052:Setd1a	UTSW	7	127,384,529 (GRCm39)	unclassified	probably benign
RF055:Setd1a	UTSW	7	127,384,471 (GRCm39)	unclassified	probably benign
RF056:Setd1a	UTSW	7	127,384,500 (GRCm39)	unclassified	probably benign
RF056:Setd1a	UTSW	7	127,384,475 (GRCm39)	unclassified	probably benign
RF058:Setd1a	UTSW	7	127,384,490 (GRCm39)	unclassified	probably benign
Z1176:Setd1a	UTSW	7	127,398,266 (GRCm39)	missense	unknown

Predicted Primers

PCR Primer
(F):5'- AAGCTGGAATCGTTACCAGC -3'
(R):5'- ACGGGAATCCAAACTGCTG -3'

Sequencing Primer
(F):5'- GCAACTAGAGAGGACCCTTCTG -3'
(R):5'- ATCCAAACTGCTGTGCTGAG -3'

Posted On

2015-02-18