Mutagenetix > Incidental Mutation

Incidental Mutation 'R0645:Setd1a'

57063

Institutional Source

Beutler Lab

Gene Symbol

Setd1a

Ensembl Gene

ENSMUSG00000042308

Gene Name

SET domain containing 1A

Synonyms

KMT2F

MMRRC Submission

038830-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0645 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

127376561-127399294 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 127386382 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Isoleucine at position 336 (V336I)

Ref Sequence

ENSEMBL: ENSMUSP00000145647 (fasta)

Gene Model

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

AlphaFold

E9PYH6

Predicted Effect

probably benign
Transcript: ENSMUST00000047075
AA Change: V879I

PolyPhen 2 Score 0.326 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000047672
Gene: ENSMUSG00000042308
AA Change: V879I

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: V879I

PolyPhen 2 Score 0.326 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000037600
Gene: ENSMUSG00000042308
AA Change: V879I

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 damaging
Transcript: ENSMUST00000154987
AA Change: V336I

PolyPhen 2 Score 0.964 (Sensitivity: 0.78; Specificity: 0.95)

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.5%

Validation Efficiency

99% (94/95)

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: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam18	G	T	8: 25,162,136 (GRCm39)	Y46*	probably null	Het
Adam26b	A	C	8: 43,973,524 (GRCm39)	C493G	probably damaging	Het
Ak5	A	T	3: 152,359,252 (GRCm39)	L182Q	probably damaging	Het
Akt1s1	T	C	7: 44,498,645 (GRCm39)		probably benign	Het
Amhr2	G	T	15: 102,354,863 (GRCm39)	G133C	probably damaging	Het
Btbd9	A	T	17: 30,743,941 (GRCm39)	L187Q	probably damaging	Het
Ccdc117	A	T	11: 5,484,385 (GRCm39)		probably benign	Het
Ccdc138	A	T	10: 58,411,542 (GRCm39)	I637F	probably damaging	Het
Ccdc162	A	G	10: 41,462,407 (GRCm39)		probably benign	Het
Cdc25b	C	A	2: 131,033,533 (GRCm39)	H157Q	probably benign	Het
Cdon	A	G	9: 35,388,379 (GRCm39)		probably null	Het
Cdt1	G	A	8: 123,298,884 (GRCm39)		probably benign	Het
Cep350	C	T	1: 155,816,458 (GRCm39)		probably null	Het
Cfb	T	C	17: 35,078,992 (GRCm39)	K831R	probably benign	Het
Cldn4	C	A	5: 134,975,645 (GRCm39)		probably benign	Het
Cntnap5b	T	C	1: 99,999,767 (GRCm39)		probably benign	Het
Cyp27b1	T	G	10: 126,884,967 (GRCm39)	S77A	probably benign	Het
Dlc1	T	C	8: 37,041,203 (GRCm39)	D1342G	possibly damaging	Het
Dlgap4	A	G	2: 156,603,799 (GRCm39)	H887R	probably damaging	Het
Duox2	A	G	2: 122,123,139 (GRCm39)	I503T	probably damaging	Het
Eml4	T	C	17: 83,770,922 (GRCm39)		probably benign	Het
Ermap	A	G	4: 119,042,888 (GRCm39)	S212P	probably benign	Het
Esrrg	T	A	1: 187,775,538 (GRCm39)	C22S	probably benign	Het
Evx2	T	A	2: 74,488,238 (GRCm39)	Y194F	possibly damaging	Het
Fbn2	T	G	18: 58,191,461 (GRCm39)	D1554A	probably damaging	Het
Flrt1	G	A	19: 7,074,508 (GRCm39)		probably benign	Het
Fndc5	A	G	4: 129,033,630 (GRCm39)		probably benign	Het
Frem1	A	T	4: 82,907,403 (GRCm39)	I837N	probably damaging	Het
Fzd10	G	T	5: 128,679,662 (GRCm39)	A461S	possibly damaging	Het
Ganab	T	A	19: 8,888,477 (GRCm39)	Y511N	probably damaging	Het
Gbp7	A	G	3: 142,243,926 (GRCm39)		probably null	Het
Gm5919	T	A	9: 83,765,436 (GRCm39)	C91S	unknown	Het
Gpr31b	A	T	17: 13,271,093 (GRCm39)	C25*	probably null	Het
Grb10	A	G	11: 11,886,755 (GRCm39)	S505P	probably damaging	Het
Grm4	A	T	17: 27,654,183 (GRCm39)	V542E	probably damaging	Het
Gsta5	T	C	9: 78,206,303 (GRCm39)	I75T	possibly damaging	Het
Hivep3	G	A	4: 119,954,531 (GRCm39)	R949H	possibly damaging	Het
Hycc1	C	T	5: 24,184,506 (GRCm39)	G242D	probably damaging	Het
Invs	A	T	4: 48,407,653 (GRCm39)	M543L	probably benign	Het
Kcnk2	T	C	1: 188,988,927 (GRCm39)		probably null	Het
Kdm6b	A	T	11: 69,295,844 (GRCm39)	S808T	unknown	Het
Klhl30	C	T	1: 91,283,228 (GRCm39)	R277W	probably damaging	Het
Lama1	A	G	17: 68,080,707 (GRCm39)	Q1245R	probably benign	Het
Lingo3	G	T	10: 80,671,169 (GRCm39)	H254N	probably benign	Het
Lzts1	A	T	8: 69,588,392 (GRCm39)	H521Q	possibly damaging	Het
Map3k19	A	C	1: 127,749,919 (GRCm39)	I1144S	possibly damaging	Het
Mast2	A	G	4: 116,165,184 (GRCm39)	S1411P	probably damaging	Het
Mast2	T	C	4: 116,170,043 (GRCm39)		probably benign	Het
Mesp1	G	T	7: 79,442,328 (GRCm39)	S225R	possibly damaging	Het
Micu1	A	G	10: 59,675,503 (GRCm39)	T366A	possibly damaging	Het
Mideas	G	T	12: 84,205,077 (GRCm39)	N834K	possibly damaging	Het
Mknk2	T	C	10: 80,507,742 (GRCm39)		probably null	Het
Msh5	A	G	17: 35,258,199 (GRCm39)	L309P	probably damaging	Het
Myo7b	T	C	18: 32,127,962 (GRCm39)	I577V	probably benign	Het
Myom2	T	A	8: 15,167,698 (GRCm39)	D1094E	probably damaging	Het
Nedd1	T	C	10: 92,527,693 (GRCm39)		probably null	Het
Neu4	T	C	1: 93,950,191 (GRCm39)	L50S	probably damaging	Het
Noa1	T	C	5: 77,457,722 (GRCm39)	Y61C	probably benign	Het
Nr1h4	A	T	10: 89,342,390 (GRCm39)	M30K	probably benign	Het
Nsd3	A	G	8: 26,199,096 (GRCm39)	I1219V	probably benign	Het
Nup188	T	A	2: 30,233,478 (GRCm39)		probably null	Het
Or10ag2	T	A	2: 87,248,612 (GRCm39)	Y71*	probably null	Het
Or5al5	A	G	2: 85,961,378 (GRCm39)	S210P	probably damaging	Het
Or6c208	T	A	10: 129,224,162 (GRCm39)	I220N	possibly damaging	Het
Or6k2	A	T	1: 173,986,920 (GRCm39)	T194S	probably benign	Het
Pbk	G	A	14: 66,051,245 (GRCm39)		probably benign	Het
Pcnx2	G	A	8: 126,487,459 (GRCm39)	T1848M	possibly damaging	Het
Pdzd7	C	T	19: 45,033,914 (GRCm39)	G57R	possibly damaging	Het
Pik3r4	C	A	9: 105,546,386 (GRCm39)		probably benign	Het
Plce1	A	G	19: 38,766,433 (GRCm39)	S2153G	probably damaging	Het
Potefam1	C	T	2: 111,044,928 (GRCm39)		probably null	Het
Pphln1	G	A	15: 93,318,192 (GRCm39)	V34M	possibly damaging	Het
Prrc2a	T	C	17: 35,375,308 (GRCm39)	D1114G	probably damaging	Het
Prss16	T	C	13: 22,193,546 (GRCm39)		probably benign	Het
Rtp3	T	C	9: 110,816,168 (GRCm39)	K128E	probably damaging	Het
Scn3a	T	A	2: 65,355,194 (GRCm39)	I241F	possibly damaging	Het
Sfpq	A	G	4: 126,916,762 (GRCm39)	I320V	possibly damaging	Het
Skint5	A	T	4: 113,620,679 (GRCm39)	D678E	unknown	Het
Slc12a9	G	A	5: 137,313,638 (GRCm39)	P774S	probably benign	Het
Slc25a54	C	G	3: 109,019,481 (GRCm39)	L362V	possibly damaging	Het
Smarcd1	A	G	15: 99,605,267 (GRCm39)		probably null	Het
Spata31e5	T	A	1: 28,816,011 (GRCm39)	N674Y	probably damaging	Het
Suco	A	T	1: 161,661,683 (GRCm39)	M916K	probably damaging	Het
Tiam2	T	C	17: 3,564,973 (GRCm39)	S1404P	possibly damaging	Het
Topors	T	C	4: 40,260,333 (GRCm39)	T984A	unknown	Het
Trabd2b	A	T	4: 114,443,767 (GRCm39)	K308M	probably damaging	Het
Trmo	A	T	4: 46,377,083 (GRCm39)		probably benign	Het
Trpc3	A	T	3: 36,725,654 (GRCm39)	D107E	probably benign	Het
Ugcg	C	T	4: 59,207,798 (GRCm39)	P46S	probably benign	Het
Uggt2	A	C	14: 119,295,010 (GRCm39)	Y539D	probably benign	Het
Wwc2	T	G	8: 48,353,674 (GRCm39)		probably benign	Het
Zdbf2	T	A	1: 63,344,109 (GRCm39)	D829E	possibly damaging	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
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
R3428:Setd1a	UTSW	7	127,384,493 (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'- GCTGCTTTACAGTGGACTGAACGC -3'
(R):5'- CCGTTTTACCTGGCAGATGCAGAC -3'

Sequencing Primer
(F):5'- GTGGATGGCCTAAATTATCAGAC -3'
(R):5'- CCTGGCAGATGCAGACAGATAG -3'

Posted On

2013-07-11