Mutagenetix > Incidental Mutation

Incidental Mutation 'RF056:Setd1a'

605274

Institutional Source

Beutler Lab

Gene Symbol

Setd1a

Ensembl Gene

ENSMUSG00000042308

Gene Name

SET domain containing 1A

Synonyms

KMT2F

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

RF056 (G1)

Quality Score

214.544

Status

Not validated

Chromosome

Chromosomal Location

127376561-127399294 bp(+) (GRCm39)

Type of Mutation

unclassified

DNA Base Change (assembly)

GTGGTGGTGGTGGTAGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGG to GTGGTGGTGGTGGTGGTGGTGGTAGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGG at 127384475 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

probably benign
Transcript: ENSMUST00000047075

SMART Domains

Protein: ENSMUSP00000047672
Gene: ENSMUSG00000042308

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

SMART Domains

Protein: ENSMUSP00000037600
Gene: ENSMUSG00000042308

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

Coding Region Coverage

1x: 99.8%
3x: 99.7%
10x: 99.3%
20x: 98.6%

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: 35 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Begain	CG	CGCCGCAG	12: 108,999,362 (GRCm39)		probably benign	Het
Bhlhb9	C	T	X: 134,791,239 (GRCm39)	L484F	possibly damaging	Het
Cacna1f	GA	GAGTA	X: 7,486,314 (GRCm39)		probably null	Het
Chga	GCA	GCATCA	12: 102,527,683 (GRCm39)		probably benign	Het
Cnpy3	CCT	CCTACT	17: 47,047,670 (GRCm39)		probably null	Het
Cyb5r4	CACACTGCCCAGGGATGTGACAGACACACTGCCCAGGGA	CACACTGCCCAGGGATGTGACAGAGACACTGCCCAGGGATGTGACAGACACACTGCCCAGGGA	9: 86,922,463 (GRCm39)		probably benign	Het
Dmkn	T	TAGAGGTGGAAGTGGTGGAAGTGGTGGA	7: 30,466,632 (GRCm39)		probably benign	Het
Efhd2	GCCGCC	GCCGCCTCCGCC	4: 141,602,078 (GRCm39)		probably benign	Het
Fam171b	C	CAGCAGA	2: 83,643,240 (GRCm39)		probably benign	Het
Garin5a	CTGAGGGAGGA	CTGAGGGAGGAAGGCTGGATCCTGGATACCTGGGTATGAGGGAGGA	7: 44,149,951 (GRCm39)		probably null	Het
Gm10181	GAGAGAGAGAGAGA	G	9: 25,000,761 (GRCm39)		probably null	Het
Gm16494	TTT	TTTT	17: 47,327,841 (GRCm39)		probably null	Het
Hsdl2	CCACAGCTGCAG	CCACAGCTGCAGCAGCAGCACAGCTGCAG	4: 59,610,647 (GRCm39)		probably null	Het
Med12l	CAG	CAGAAG	3: 59,183,414 (GRCm39)		probably benign	Het
Nelfe	A	AGCGGGATCGAGACAGAGACAAAGG	17: 35,073,047 (GRCm39)		probably benign	Het
Ngfr	CAGG	C	11: 95,478,337 (GRCm39)		probably benign	Het
Nusap1	GTTAGCAGTGAGGAGCAAGCTGAGA	GTTAGCAGTGAGGAGCAAGCTGAGATACACTTTAGCAGTGAGGAGCAAGCTGAGA	2: 119,458,067 (GRCm39)		probably benign	Het
Nusap1	TACACGTTAGCAGTGAGGAGCAAGCTGAGAC	TACACGTTAGCAGTGAGGAGCAAGCTGAGACACACGTTAGCAGTGAGGAGCAAGCTGAGAC	2: 119,458,062 (GRCm39)		probably benign	Het
Nusap1	CAGTGAGGAGCAAGCTGAGA	CAGTGAGGAGCAAGCTGAGATACACGTTAGGAGTGAGGAGCAAGCTGAGA	2: 119,458,072 (GRCm39)		probably benign	Het
Or10n7-ps1	A	ATAGG	9: 39,598,050 (GRCm39)		probably null	Het
Pdik1l	TTGCACC	TTGCACCTGCACC	4: 134,006,813 (GRCm39)		probably benign	Het
Pdik1l	C	CCACCAA	4: 134,006,827 (GRCm39)		probably benign	Het
Pqbp1	ACACACACACACC	A	X: 7,764,998 (GRCm39)		probably benign	Het
Rbm28	AGCAACACCTCTCACCTGGGGCAGAAGCA	AGCAACACCTCTCACCTGGGGCAGAAGCAACACCTCTCACCTGGGGCAGAAGCA	6: 29,157,052 (GRCm39)		probably null	Het
Rnf126	GAGGAC	G	10: 79,594,976 (GRCm39)		probably null	Het
Rprd2	CAGAGCCTGTGGTGCTCGCAGG	C	3: 95,673,631 (GRCm39)		probably benign	Het
Rtbdn	CGG	CGGAAGAGG	8: 85,682,799 (GRCm39)		probably benign	Het
Rtbdn	GCAGCG	GCAGCGCCAGCG	8: 85,682,801 (GRCm39)		probably benign	Het
Sbp	ACAAAGATGCTGACA	ACAAAGATGCTGACAGCAAAGATGCTGACA	17: 24,164,340 (GRCm39)		probably benign	Het
Sh3pxd2b	CCTGTG	CCTGTGGCTGTG	11: 32,373,055 (GRCm39)		probably benign	Het
Taf1a	CACGTTGAAGCTGTAGGTAAGTGAGACAGCGTTGAAGCTGTAGGTAAGTGAGACA	CGCGTTGAAGCTGTAGGTAAGTGAGACA	1: 183,172,369 (GRCm39)		probably benign	Het
Tcof1	TCCCCTTGGC	TCCCCTTGGCTGCTGAGATGGGCACTTTCCTAGAGACCCCCTTGGC	18: 60,966,647 (GRCm39)		probably benign	Het
Tsen2	CCAG	CCAGCAG	6: 115,537,025 (GRCm39)		probably benign	Het
Unc13b	CAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGC	CAGAGCCAGAGCCAGAGCAAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGC	4: 43,177,359 (GRCm39)		probably benign	Het
Zfp384	CCCAGGC	CCCAGGCCCAGGGCCAGGC	6: 125,013,453 (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
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
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'- GAATCGTTACCAGCGCCATACTTC -3'
(R):5'- ATCCAAACTGCTGTGCTGAG -3'

Posted On

2019-12-04