Mutagenetix > Incidental Mutation

Incidental Mutation 'R5059:Kdm3b'

470014

Institutional Source

Beutler Lab

Gene Symbol

Kdm3b

Ensembl Gene

ENSMUSG00000038773

Gene Name

KDM3B lysine (K)-specific demethylase 3B

Synonyms

Jmjd1b, 5830462I21Rik, JHDM2B

MMRRC Submission

042649-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.943) question?

Stock #

R5059 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

34910100-34971713 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 34910250 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 23 (S23P)

Ref Sequence

ENSEMBL: ENSMUSP00000153446 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000043775] [ENSMUST00000049281] [ENSMUST00000097622] [ENSMUST00000224715] [ENSMUST00000225195]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000043775
AA Change: S23P

PolyPhen 2 Score 0.208 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000037628
Gene: ENSMUSG00000038773
AA Change: S23P

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

probably benign
Transcript: ENSMUST00000049281

SMART Domains

Protein: ENSMUSP00000037034
Gene: ENSMUSG00000034300

Domain	Start	End	E-Value	Type
Pfam:FAM53	1	307	3.9e-87	PFAM
low complexity region	334	346	N/A	INTRINSIC
low complexity region	348	370	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000097622

SMART Domains

Protein: ENSMUSP00000095226
Gene: ENSMUSG00000034300

Domain	Start	End	E-Value	Type
Pfam:FAM53	1	307	1.9e-87	PFAM
low complexity region	334	346	N/A	INTRINSIC
low complexity region	348	370	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000224715
AA Change: S23P

PolyPhen 2 Score 0.794 (Sensitivity: 0.85; Specificity: 0.93)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225047

Predicted Effect

possibly damaging
Transcript: ENSMUST00000225195
AA Change: S23P

PolyPhen 2 Score 0.827 (Sensitivity: 0.84; Specificity: 0.93)

Meta Mutation Damage Score

0.0617

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 93.9%

Validation Efficiency

98% (52/53)

Allele List at MGI

Other mutations in this stock

Total: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam26b	T	A	8: 43,973,637 (GRCm39)	N455I	probably damaging	Het
Alg12	A	G	15: 88,695,659 (GRCm39)	F279S	probably damaging	Het
Angpt4	A	G	2: 151,776,360 (GRCm39)	D296G	probably damaging	Het
Ank1	T	A	8: 23,586,204 (GRCm39)	S437T	probably damaging	Het
Apol7a	G	A	15: 77,274,012 (GRCm39)		probably benign	Het
Arhgef38	T	A	3: 132,843,175 (GRCm39)	Y465F	probably damaging	Het
Atp8a2	T	G	14: 59,928,986 (GRCm39)	T1023P	probably benign	Het
Cdh20	C	A	1: 109,993,430 (GRCm39)	A295E	probably damaging	Het
Cela3b	T	C	4: 137,152,181 (GRCm39)	E92G	probably benign	Het
Cntnap5a	T	C	1: 116,356,224 (GRCm39)	S752P	probably benign	Het
Dlx2	T	C	2: 71,376,585 (GRCm39)	H51R	probably damaging	Het
Dnm2	T	C	9: 21,415,874 (GRCm39)	I736T	probably damaging	Het
Dst	A	G	1: 34,202,427 (GRCm39)	T252A	possibly damaging	Het
Fbxo40	T	C	16: 36,790,658 (GRCm39)	R151G	possibly damaging	Het
Gapdhs	C	T	7: 30,431,410 (GRCm39)	A357T	probably benign	Het
Gon4l	T	A	3: 88,807,319 (GRCm39)	M1671K	probably benign	Het
Gpi1	T	C	7: 33,907,113 (GRCm39)	Y327C	probably damaging	Het
Gucy2g	T	C	19: 55,214,503 (GRCm39)	R542G	probably benign	Het
Hectd3	A	G	4: 116,854,361 (GRCm39)	K308E	possibly damaging	Het
Hip1	A	G	5: 135,478,675 (GRCm39)	F178S	probably damaging	Het
Hydin	A	G	8: 111,232,401 (GRCm39)	D1640G	probably damaging	Het
Il18r1	G	A	1: 40,520,227 (GRCm39)		probably null	Het
Lactb	T	C	9: 66,882,426 (GRCm39)	E83G	probably benign	Het
Larp4	A	T	15: 99,903,171 (GRCm39)	D414V	probably damaging	Het
Map2k5	T	C	9: 63,164,296 (GRCm39)	H336R	probably benign	Het
Mast4	T	C	13: 102,887,071 (GRCm39)	E1006G	probably damaging	Het
Mbd5	T	C	2: 49,146,467 (GRCm39)	S226P	probably damaging	Het
Micall1	A	T	15: 79,007,034 (GRCm39)		probably benign	Het
Mtpap	T	A	18: 4,375,827 (GRCm39)		probably benign	Het
Or52ae7	A	T	7: 103,119,488 (GRCm39)	K81*	probably null	Het
Or5p58	A	G	7: 107,694,522 (GRCm39)	L85P	probably damaging	Het
Pnrc1	G	A	4: 33,246,072 (GRCm39)	Q296*	probably null	Het
Poc1a	G	T	9: 106,227,012 (GRCm39)		probably benign	Het
Pramel28	A	G	4: 143,691,565 (GRCm39)	V386A	probably damaging	Het
Prkcsh	T	A	9: 21,924,046 (GRCm39)	L439Q	probably damaging	Het
Prkdc	T	C	16: 15,655,882 (GRCm39)	L3970P	probably damaging	Het
Ptcd1	G	A	5: 145,089,034 (GRCm39)	P542L	probably benign	Het
Rps6ka5	G	A	12: 100,520,634 (GRCm39)	T631I	probably damaging	Het
Rxfp1	T	C	3: 79,570,619 (GRCm39)	N271S	probably benign	Het
Taf6	A	G	5: 138,177,709 (GRCm39)	M541T	probably benign	Het
Tek	T	A	4: 94,692,551 (GRCm39)	C169S	probably benign	Het
Tgfbr3l	T	A	8: 4,299,343 (GRCm39)		probably null	Het
Trpv3	A	G	11: 73,186,149 (GRCm39)	N647D	probably benign	Het
Ube3c	A	G	5: 29,836,293 (GRCm39)	K638R	probably null	Het
Vmn1r191	G	A	13: 22,363,163 (GRCm39)	A197V	probably damaging	Het
Vmn2r6	T	C	3: 64,445,044 (GRCm39)	T894A	possibly damaging	Het
Vstm4	T	G	14: 32,585,687 (GRCm39)	Y85D	probably damaging	Het
Wnt7a	A	G	6: 91,371,482 (GRCm39)	I160T	probably benign	Het
Zc3h7a	TAGAGAG	TAGAGAGAG	16: 10,978,985 (GRCm39)		probably null	Het
Zfp988	A	T	4: 147,416,372 (GRCm39)	K269*	probably null	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
R0941:Kdm3b	UTSW	18	34,936,605 (GRCm39)	missense	probably damaging	0.99
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
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'- GGAAATTGCAATTCCCCTCC -3'
(R):5'- AGCAGCAACAGCAGCTCTTC -3'

Sequencing Primer
(F):5'- GTGCAGCCCTGGTTGAG -3'
(R):5'- AGCAGCTCTTCGCACCC -3'

Posted On

2017-03-06