Mutagenetix > Incidental Mutation

Incidental Mutation 'R0941:Kdm3b'

82598

Institutional Source

Beutler Lab

Gene Symbol

Kdm3b

Ensembl Gene

ENSMUSG00000038773

Gene Name

KDM3B lysine (K)-specific demethylase 3B

Synonyms

Jmjd1b, 5830462I21Rik, JHDM2B

MMRRC Submission

039080-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.943) question?

Stock #

R0941 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

34910100-34971713 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 34936605 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Serine at position 296 (C296S)

Ref Sequence

ENSEMBL: ENSMUSP00000153295 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000043775] [ENSMUST00000224715] [ENSMUST00000225195]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000043775
AA Change: C296S

PolyPhen 2 Score 0.650 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000037628
Gene: ENSMUSG00000038773
AA Change: C296S

Domain	Start	End	E-Value	Type
low complexity region	20	36	N/A	INTRINSIC
Blast:JmjC	149	944	N/A	BLAST
Blast:JmjC	946	1064	5e-40	BLAST
Blast:JmjC	1069	1471	N/A	BLAST
JmjC	1499	1722	2.43e-65	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000180512

Predicted Effect

probably damaging
Transcript: ENSMUST00000224715
AA Change: C296S

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225047

Predicted Effect

probably benign
Transcript: ENSMUST00000225195

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225260

Meta Mutation Damage Score

0.0737

Coding Region Coverage

1x: 99.4%
3x: 98.7%
10x: 96.9%
20x: 93.9%

Validation Efficiency

97% (36/37)

Allele List at MGI

Other mutations in this stock

Total: 34 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acaa2	G	T	18: 74,931,414 (GRCm39)	M203I	probably benign	Het
Afmid	T	A	11: 117,726,071 (GRCm39)		probably benign	Het
Ahnak	A	G	19: 8,987,278 (GRCm39)	D2854G	probably damaging	Het
Amotl1	A	C	9: 14,507,854 (GRCm39)	I31S	possibly damaging	Het
Arf3	A	G	15: 98,638,984 (GRCm39)	V91A	probably benign	Het
Atp1b1	A	C	1: 164,270,829 (GRCm39)	I50S	probably benign	Het
Baz1a	A	T	12: 54,945,216 (GRCm39)	S1380T	probably benign	Het
C4b	T	A	17: 34,959,029 (GRCm39)	T467S	probably benign	Het
Casd1	T	C	6: 4,635,848 (GRCm39)	S640P	probably damaging	Het
Col4a1	C	T	8: 11,258,296 (GRCm39)	G1396S	unknown	Het
Extl1	TGCGTTGCACCGATACCGGG	TG	4: 134,084,988 (GRCm39)		probably benign	Het
Fhip1a	G	T	3: 85,580,366 (GRCm39)	P613Q	probably benign	Het
Gm12695	C	A	4: 96,616,454 (GRCm39)	E460*	probably null	Het
Gnmt	A	G	17: 47,037,271 (GRCm39)	L171P	probably damaging	Het
Gpc1	G	A	1: 92,785,031 (GRCm39)	R358H	possibly damaging	Het
Igsf8	C	T	1: 172,143,963 (GRCm39)	R39C	probably damaging	Het
Lama1	C	T	17: 68,082,860 (GRCm39)	P1373S	probably benign	Het
Lamc1	A	G	1: 153,208,020 (GRCm39)	L89P	possibly damaging	Het
Ltc4s	T	G	11: 50,128,269 (GRCm39)		probably null	Het
Met	A	T	6: 17,491,393 (GRCm39)	I52F	probably damaging	Het
Mterf2	G	A	10: 84,955,934 (GRCm39)	T230M	possibly damaging	Het
Mybpc2	T	C	7: 44,156,311 (GRCm39)	K834R	probably benign	Het
Npr1	A	T	3: 90,368,716 (GRCm39)	I448N	probably benign	Het
Or52u1	C	T	7: 104,237,545 (GRCm39)	T178I	probably damaging	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Serpini1	A	T	3: 75,523,934 (GRCm39)	I181F	probably damaging	Het
Shc3	T	C	13: 51,634,242 (GRCm39)	M88V	probably benign	Het
Skint6	T	A	4: 113,095,555 (GRCm39)	S35C	probably damaging	Het
Spta1	T	C	1: 174,072,771 (GRCm39)		probably benign	Het
Sult2a2	C	T	7: 13,468,815 (GRCm39)	R94*	probably null	Het
Trim9	A	G	12: 70,295,037 (GRCm39)	V787A	probably damaging	Het
Ttn	A	G	2: 76,549,367 (GRCm39)	V31770A	probably benign	Het
Unc5d	T	C	8: 29,249,055 (GRCm39)	N337D	possibly damaging	Het
Vmn2r7	A	T	3: 64,624,000 (GRCm39)	Y107N	probably benign	Het

Other mutations in Kdm3b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00162:Kdm3b	APN	18	34,942,462 (GRCm39)	missense	probably benign	0.03
IGL01357:Kdm3b	APN	18	34,926,067 (GRCm39)	missense	probably damaging	1.00
IGL01615:Kdm3b	APN	18	34,962,284 (GRCm39)	missense	probably damaging	1.00
IGL01980:Kdm3b	APN	18	34,967,289 (GRCm39)	missense	probably damaging	1.00
IGL02277:Kdm3b	APN	18	34,956,717 (GRCm39)	missense	probably damaging	1.00
IGL02346:Kdm3b	APN	18	34,967,291 (GRCm39)	missense	probably damaging	1.00
IGL02417:Kdm3b	APN	18	34,941,630 (GRCm39)	missense	probably benign	0.03
IGL02531:Kdm3b	APN	18	34,928,782 (GRCm39)	missense	probably benign
IGL02589:Kdm3b	APN	18	34,945,471 (GRCm39)	missense	possibly damaging	0.89
IGL02793:Kdm3b	APN	18	34,962,072 (GRCm39)	missense	probably damaging	0.99
IGL03121:Kdm3b	APN	18	34,928,762 (GRCm39)	missense	probably damaging	0.98
IGL03123:Kdm3b	APN	18	34,942,544 (GRCm39)	critical splice donor site	probably null
IGL03128:Kdm3b	APN	18	34,960,480 (GRCm39)	missense	probably damaging	1.00
Affable	UTSW	18	34,926,058 (GRCm39)	missense	probably damaging	1.00
Dotage	UTSW	18	34,960,435 (GRCm39)	missense	probably damaging	1.00
Endearing	UTSW	18	34,960,381 (GRCm39)	splice site	probably null
Oldtimer	UTSW	18	34,956,752 (GRCm39)	nonsense	probably null
PIT4382001:Kdm3b	UTSW	18	34,942,140 (GRCm39)	missense	probably damaging	1.00
PIT4445001:Kdm3b	UTSW	18	34,926,168 (GRCm39)	nonsense	probably null
R0068:Kdm3b	UTSW	18	34,957,827 (GRCm39)	missense	probably benign	0.18
R0068:Kdm3b	UTSW	18	34,957,827 (GRCm39)	missense	probably benign	0.18
R0233:Kdm3b	UTSW	18	34,942,473 (GRCm39)	missense	probably damaging	0.97
R0265:Kdm3b	UTSW	18	34,928,716 (GRCm39)	splice site	probably benign
R0306:Kdm3b	UTSW	18	34,937,070 (GRCm39)	missense	probably benign	0.35
R0970:Kdm3b	UTSW	18	34,942,092 (GRCm39)	missense	probably damaging	1.00
R1061:Kdm3b	UTSW	18	34,929,915 (GRCm39)	missense	probably damaging	1.00
R1104:Kdm3b	UTSW	18	34,952,864 (GRCm39)	missense	probably damaging	1.00
R1221:Kdm3b	UTSW	18	34,941,298 (GRCm39)	missense	possibly damaging	0.57
R1486:Kdm3b	UTSW	18	34,967,357 (GRCm39)	missense	probably damaging	1.00
R1523:Kdm3b	UTSW	18	34,926,226 (GRCm39)	critical splice donor site	probably null
R1558:Kdm3b	UTSW	18	34,942,149 (GRCm39)	missense	probably damaging	1.00
R1585:Kdm3b	UTSW	18	34,942,345 (GRCm39)	missense	probably damaging	1.00
R1601:Kdm3b	UTSW	18	34,941,784 (GRCm39)	missense	probably damaging	1.00
R1650:Kdm3b	UTSW	18	34,942,168 (GRCm39)	missense	possibly damaging	0.93
R1772:Kdm3b	UTSW	18	34,936,557 (GRCm39)	missense	probably benign	0.01
R1853:Kdm3b	UTSW	18	34,966,446 (GRCm39)	missense	probably damaging	1.00
R1934:Kdm3b	UTSW	18	34,946,597 (GRCm39)	missense	probably benign	0.04
R1959:Kdm3b	UTSW	18	34,945,448 (GRCm39)	missense	possibly damaging	0.55
R2079:Kdm3b	UTSW	18	34,936,570 (GRCm39)	missense	probably damaging	1.00
R2102:Kdm3b	UTSW	18	34,963,200 (GRCm39)	missense	probably damaging	1.00
R2121:Kdm3b	UTSW	18	34,929,833 (GRCm39)	splice site	probably benign
R2281:Kdm3b	UTSW	18	34,941,472 (GRCm39)	missense	probably damaging	1.00
R3719:Kdm3b	UTSW	18	34,941,724 (GRCm39)	missense	probably damaging	1.00
R3755:Kdm3b	UTSW	18	34,941,349 (GRCm39)	missense	probably benign
R3857:Kdm3b	UTSW	18	34,966,440 (GRCm39)	missense	probably benign
R4165:Kdm3b	UTSW	18	34,928,797 (GRCm39)	missense	probably benign	0.01
R4166:Kdm3b	UTSW	18	34,928,797 (GRCm39)	missense	probably benign	0.01
R4372:Kdm3b	UTSW	18	34,960,497 (GRCm39)	missense	probably benign	0.00
R4672:Kdm3b	UTSW	18	34,941,630 (GRCm39)	missense	probably benign
R4933:Kdm3b	UTSW	18	34,943,446 (GRCm39)	missense	probably damaging	1.00
R4969:Kdm3b	UTSW	18	34,955,428 (GRCm39)	missense	probably damaging	1.00
R5009:Kdm3b	UTSW	18	34,957,763 (GRCm39)	missense	probably benign	0.42
R5059:Kdm3b	UTSW	18	34,910,250 (GRCm39)	missense	possibly damaging	0.83
R5092:Kdm3b	UTSW	18	34,946,515 (GRCm39)	missense	probably benign	0.16
R5270:Kdm3b	UTSW	18	34,960,467 (GRCm39)	missense	probably damaging	1.00
R5816:Kdm3b	UTSW	18	34,961,522 (GRCm39)	missense	probably damaging	0.99
R5970:Kdm3b	UTSW	18	34,962,342 (GRCm39)	missense	probably damaging	1.00
R6244:Kdm3b	UTSW	18	34,926,058 (GRCm39)	missense	probably damaging	1.00
R6705:Kdm3b	UTSW	18	34,952,926 (GRCm39)	missense	probably damaging	1.00
R6723:Kdm3b	UTSW	18	34,926,058 (GRCm39)	missense	probably damaging	0.99
R6909:Kdm3b	UTSW	18	34,960,381 (GRCm39)	splice site	probably null
R6958:Kdm3b	UTSW	18	34,941,336 (GRCm39)	missense	probably benign	0.00
R7026:Kdm3b	UTSW	18	34,955,517 (GRCm39)	missense	possibly damaging	0.90
R7289:Kdm3b	UTSW	18	34,927,557 (GRCm39)	missense	probably benign	0.00
R7488:Kdm3b	UTSW	18	34,957,934 (GRCm39)	missense	probably damaging	0.97
R7587:Kdm3b	UTSW	18	34,930,080 (GRCm39)	splice site	probably null
R7695:Kdm3b	UTSW	18	34,927,612 (GRCm39)	missense	possibly damaging	0.86
R7846:Kdm3b	UTSW	18	34,942,293 (GRCm39)	missense	possibly damaging	0.94
R7984:Kdm3b	UTSW	18	34,956,752 (GRCm39)	nonsense	probably null
R7997:Kdm3b	UTSW	18	34,941,336 (GRCm39)	missense	probably benign	0.00
R8035:Kdm3b	UTSW	18	34,941,781 (GRCm39)	missense	probably damaging	1.00
R8064:Kdm3b	UTSW	18	34,946,460 (GRCm39)	critical splice acceptor site	probably null
R8141:Kdm3b	UTSW	18	34,961,599 (GRCm39)	nonsense	probably null
R8302:Kdm3b	UTSW	18	34,967,388 (GRCm39)	missense	probably damaging	1.00
R8328:Kdm3b	UTSW	18	34,926,123 (GRCm39)	missense	probably damaging	1.00
R8443:Kdm3b	UTSW	18	34,926,129 (GRCm39)	missense	probably benign	0.04
R8513:Kdm3b	UTSW	18	34,926,129 (GRCm39)	missense	probably benign	0.04
R8515:Kdm3b	UTSW	18	34,926,129 (GRCm39)	missense	probably benign	0.04
R8523:Kdm3b	UTSW	18	34,926,129 (GRCm39)	missense	probably benign	0.04
R8717:Kdm3b	UTSW	18	34,952,840 (GRCm39)	missense	probably damaging	0.98
R8725:Kdm3b	UTSW	18	34,960,435 (GRCm39)	missense	probably damaging	1.00
R8727:Kdm3b	UTSW	18	34,960,435 (GRCm39)	missense	probably damaging	1.00
R8762:Kdm3b	UTSW	18	34,937,157 (GRCm39)	missense	probably benign
R8835:Kdm3b	UTSW	18	34,941,802 (GRCm39)	missense	probably damaging	1.00
R8918:Kdm3b	UTSW	18	34,970,650 (GRCm39)	missense	probably damaging	1.00
R9015:Kdm3b	UTSW	18	34,963,212 (GRCm39)	missense	probably damaging	1.00
R9144:Kdm3b	UTSW	18	34,927,558 (GRCm39)	missense	probably benign
R9246:Kdm3b	UTSW	18	34,941,480 (GRCm39)	nonsense	probably null
R9376:Kdm3b	UTSW	18	34,970,718 (GRCm39)	missense	probably damaging	0.99
X0028:Kdm3b	UTSW	18	34,932,319 (GRCm39)	splice site	probably null
X0067:Kdm3b	UTSW	18	34,956,570 (GRCm39)	missense	probably benign	0.00
Z1176:Kdm3b	UTSW	18	34,942,122 (GRCm39)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- TGTCTTAGAGCAGCATCAGAGCGG -3'
(R):5'- TGTGGCTGAAGCATACGGAGTG -3'

Sequencing Primer
(F):5'- AGCGGTGCCTGCTCTAAATG -3'
(R):5'- GGCTCATCCTGTACCACCAG -3'

Posted On

2013-11-08