Mutagenetix > Incidental Mutation

Incidental Mutation 'R7704:Kdm5b'

594168

Institutional Source

Beutler Lab

Gene Symbol

Kdm5b

Ensembl Gene

ENSMUSG00000042207

Gene Name

lysine demethylase 5B

Synonyms

2010009J12Rik, PLU-1, Rb-Bp2, Jarid1b, D1Ertd202e, Plu1, 2210016I17Rik

MMRRC Submission

045765-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.451) question?

Stock #

R7704 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

134487916-134560621 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 134515669 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Cysteine at position 98 (R98C)

Ref Sequence

ENSEMBL: ENSMUSP00000038138 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047714] [ENSMUST00000112198]

AlphaFold

Q80Y84

Predicted Effect

probably damaging
Transcript: ENSMUST00000047714
AA Change: R98C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000038138
Gene: ENSMUSG00000042207
AA Change: R98C

Domain	Start	End	E-Value	Type
low complexity region	7	30	N/A	INTRINSIC
JmjN	31	72	2.87e-20	SMART
ARID	94	183	7.39e-32	SMART
BRIGHT	98	188	1.51e-35	SMART
low complexity region	228	239	N/A	INTRINSIC
PHD	311	357	6.15e-14	SMART
JmjC	453	619	2.33e-67	SMART
Pfam:zf-C5HC2	692	744	2.2e-17	PFAM
Pfam:PLU-1	757	1088	5.6e-92	PFAM
low complexity region	1097	1109	N/A	INTRINSIC
PHD	1178	1222	6.2e-10	SMART
low complexity region	1225	1236	N/A	INTRINSIC
low complexity region	1406	1417	N/A	INTRINSIC
low complexity region	1470	1484	N/A	INTRINSIC
PHD	1486	1536	1.18e-6	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000112198
AA Change: R98C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000107817
Gene: ENSMUSG00000042207
AA Change: R98C

Domain	Start	End	E-Value	Type
low complexity region	7	30	N/A	INTRINSIC
JmjN	31	72	2.87e-20	SMART
ARID	94	183	7.39e-32	SMART
BRIGHT	98	188	1.51e-35	SMART
low complexity region	228	239	N/A	INTRINSIC
PHD	311	357	6.15e-14	SMART
JmjC	453	619	2.33e-67	SMART
Pfam:zf-C5HC2	692	745	6.7e-21	PFAM
Pfam:PLU-1	756	1088	6e-94	PFAM
low complexity region	1097	1109	N/A	INTRINSIC
PHD	1178	1222	6.2e-10	SMART
low complexity region	1225	1236	N/A	INTRINSIC
low complexity region	1406	1417	N/A	INTRINSIC
low complexity region	1470	1484	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

MGI Phenotype

FUNCTION: This gene encodes a lysine-specific histone demethylase that belongs to the jumonji/ARID domain-containing family of histone demethylases. The encoded protein is capable of demethylating tri-, di- and monomethylated lysine 4 of histone H3. This protein plays a role in the transcriptional repression or certain tumor suppressor genes and is upregulated in certain cancer cells. This protein may also play a role in genome stability and DNA repair. Homozygous mutant mice display decreased body weight, decreased female fertility, lower uterine weight, and a delay in mammary development. Knockout of this gene has also been associated with embryonic lethality. [provided by RefSeq, Dec 2016]
PHENOTYPE: Mice homozygous for a gene trapped allele exhibit decreased body weight, background-sensitive premature mortality, decreased female fertility, delayed mammary gland development, decreased serum estradiol levels, and reduced mammary epithelial cell proliferation in early puberty. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 49 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc8	C	A	7: 45,756,068 (GRCm39)	W1458L	probably damaging	Het
Actn4	A	T	7: 28,596,467 (GRCm39)	I676N	possibly damaging	Het
Adamts10	T	C	17: 33,770,126 (GRCm39)	C1002R	probably damaging	Het
Agbl2	A	C	2: 90,619,349 (GRCm39)	N58T	probably benign	Het
Akap12	A	T	10: 4,306,082 (GRCm39)	D1069V	probably damaging	Het
Bltp2	C	A	11: 78,159,570 (GRCm39)	Q540K	probably benign	Het
Cfap65	T	A	1: 74,967,527 (GRCm39)	T184S	probably benign	Het
Chd1	T	C	17: 15,987,737 (GRCm39)	V1517A	probably benign	Het
CN725425	T	A	15: 91,119,993 (GRCm39)	V38D	possibly damaging	Het
Copg1	T	A	6: 87,884,940 (GRCm39)	L712Q	probably benign	Het
Ctsf	T	G	19: 4,906,567 (GRCm39)	F165V	probably damaging	Het
Ddx21	T	C	10: 62,429,865 (GRCm39)	Y293C	probably damaging	Het
Ddx46	C	T	13: 55,821,832 (GRCm39)	P839S	probably benign	Het
Dennd5a	A	G	7: 109,496,174 (GRCm39)	V1164A	possibly damaging	Het
Dync1h1	T	A	12: 110,632,200 (GRCm39)	I4490N	probably damaging	Het
Ecm1	A	C	3: 95,643,843 (GRCm39)	Y236D	probably damaging	Het
Fat2	T	C	11: 55,175,173 (GRCm39)	T1847A	probably benign	Het
Galc	T	A	12: 98,175,102 (GRCm39)	I567L	probably benign	Het
Gask1a	C	T	9: 121,780,151 (GRCm39)		probably benign	Het
H6pd	T	C	4: 150,067,360 (GRCm39)	D350G	probably benign	Het
Ifi44	A	G	3: 151,438,061 (GRCm39)	Y409H	probably benign	Het
Kdm5a	T	G	6: 120,404,025 (GRCm39)	F1210C	probably damaging	Het
Lipt1	T	A	1: 37,915,043 (GRCm39)	C366*	probably null	Het
Med13	G	A	11: 86,236,744 (GRCm39)	R138*	probably null	Het
Mterf1a	A	G	5: 3,941,845 (GRCm39)	C8R	probably benign	Het
Ncapg2	A	T	12: 116,382,897 (GRCm39)	I243F	probably damaging	Het
Nop58	T	C	1: 59,744,754 (GRCm39)	S304P	probably damaging	Het
Nsd2	T	C	5: 34,028,811 (GRCm39)	*167Q	probably null	Het
Or1e30	T	G	11: 73,678,616 (GRCm39)	M284R	probably damaging	Het
Or2t35	T	A	14: 14,407,867 (GRCm38)	I213N	probably damaging	Het
Or52ab2	T	A	7: 102,969,978 (GRCm39)	M120K		Het
Pramel29	C	T	4: 143,935,091 (GRCm39)	V217I	possibly damaging	Het
Prdm16	C	T	4: 154,425,947 (GRCm39)	G613R	probably damaging	Het
Prss46	T	C	9: 110,679,065 (GRCm39)	S89P	probably damaging	Het
Scin	T	C	12: 40,174,687 (GRCm39)	N132S	possibly damaging	Het
Sec14l2	T	C	11: 4,058,574 (GRCm39)	K196R	probably benign	Het
Sox17	C	A	1: 4,563,895 (GRCm39)		probably benign	Het
Tango6	A	G	8: 107,425,621 (GRCm39)	T394A	probably benign	Het
Tbc1d22a	T	A	15: 86,250,876 (GRCm39)	I398N	probably damaging	Het
Tdpoz8	A	G	3: 92,981,752 (GRCm39)	I183V	probably benign	Het
Tmem8b	T	C	4: 43,689,461 (GRCm39)	V285A	probably damaging	Het
Tnfrsf11b	T	A	15: 54,123,497 (GRCm39)	T35S	probably benign	Het
Unc13c	T	A	9: 73,606,494 (GRCm39)	I1289F	probably benign	Het
Ust	C	T	10: 8,205,987 (GRCm39)	V99I	probably benign	Het
Vmn1r76	A	G	7: 11,664,344 (GRCm39)	V290A	probably benign	Het
Vmn2r50	T	C	7: 9,781,665 (GRCm39)	N360S	probably benign	Het
Vmn2r93	T	C	17: 18,536,910 (GRCm39)	I531T	probably benign	Het
Zap70	T	C	1: 36,818,395 (GRCm39)		probably null	Het
Zfp932	A	G	5: 110,157,630 (GRCm39)	N443D	probably benign	Het

Other mutations in Kdm5b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00230:Kdm5b	APN	1	134,548,693 (GRCm39)	missense	probably damaging	1.00
IGL01458:Kdm5b	APN	1	134,549,724 (GRCm39)	missense	possibly damaging	0.53
IGL01567:Kdm5b	APN	1	134,530,278 (GRCm39)	missense	probably damaging	1.00
IGL01625:Kdm5b	APN	1	134,545,706 (GRCm39)	missense	possibly damaging	0.74
IGL01970:Kdm5b	APN	1	134,528,465 (GRCm39)	missense	probably damaging	1.00
IGL02183:Kdm5b	APN	1	134,552,669 (GRCm39)	missense	probably benign	0.09
IGL02592:Kdm5b	APN	1	134,552,591 (GRCm39)	missense	probably damaging	0.99
IGL02695:Kdm5b	APN	1	134,532,223 (GRCm39)	missense	possibly damaging	0.94
IGL02697:Kdm5b	APN	1	134,516,511 (GRCm39)	splice site	probably benign
IGL03036:Kdm5b	APN	1	134,536,675 (GRCm39)	missense	probably damaging	1.00
IGL03056:Kdm5b	APN	1	134,515,717 (GRCm39)	missense	probably damaging	0.99
IGL03206:Kdm5b	APN	1	134,555,055 (GRCm39)	missense	probably benign
IGL03342:Kdm5b	APN	1	134,530,314 (GRCm39)	missense	probably benign	0.00
IGL03388:Kdm5b	APN	1	134,555,060 (GRCm39)	missense	probably benign
amaryllis	UTSW	1	134,536,799 (GRCm39)	critical splice donor site	probably null
PIT4486001:Kdm5b	UTSW	1	134,556,423 (GRCm39)	missense	probably damaging	1.00
R0233:Kdm5b	UTSW	1	134,532,372 (GRCm39)	splice site	probably benign
R0334:Kdm5b	UTSW	1	134,532,260 (GRCm39)	missense	probably damaging	0.99
R0504:Kdm5b	UTSW	1	134,548,761 (GRCm39)	critical splice donor site	probably null
R0505:Kdm5b	UTSW	1	134,530,309 (GRCm39)	missense	probably damaging	0.96
R0521:Kdm5b	UTSW	1	134,545,771 (GRCm39)	missense	possibly damaging	0.65
R1004:Kdm5b	UTSW	1	134,516,642 (GRCm39)	missense	possibly damaging	0.71
R1087:Kdm5b	UTSW	1	134,528,375 (GRCm39)	missense	probably damaging	1.00
R1126:Kdm5b	UTSW	1	134,541,729 (GRCm39)	missense	possibly damaging	0.90
R1221:Kdm5b	UTSW	1	134,526,829 (GRCm39)	missense	probably damaging	0.98
R1230:Kdm5b	UTSW	1	134,540,992 (GRCm39)	missense	probably damaging	1.00
R1345:Kdm5b	UTSW	1	134,558,288 (GRCm39)	missense	possibly damaging	0.94
R1482:Kdm5b	UTSW	1	134,552,635 (GRCm39)	missense	probably damaging	1.00
R1582:Kdm5b	UTSW	1	134,552,591 (GRCm39)	missense	probably damaging	0.99
R1653:Kdm5b	UTSW	1	134,530,219 (GRCm39)	missense	probably damaging	1.00
R1693:Kdm5b	UTSW	1	134,525,314 (GRCm39)	splice site	probably benign
R1721:Kdm5b	UTSW	1	134,540,919 (GRCm39)	splice site	probably benign
R1741:Kdm5b	UTSW	1	134,545,755 (GRCm39)	missense	possibly damaging	0.82
R1762:Kdm5b	UTSW	1	134,532,205 (GRCm39)	nonsense	probably null
R1820:Kdm5b	UTSW	1	134,525,408 (GRCm39)	missense	possibly damaging	0.87
R1872:Kdm5b	UTSW	1	134,552,732 (GRCm39)	missense	probably damaging	1.00
R1966:Kdm5b	UTSW	1	134,541,611 (GRCm39)	splice site	probably null
R2056:Kdm5b	UTSW	1	134,540,952 (GRCm39)	missense	probably benign	0.05
R2059:Kdm5b	UTSW	1	134,540,952 (GRCm39)	missense	probably benign	0.05
R2405:Kdm5b	UTSW	1	134,536,754 (GRCm39)	missense	probably damaging	0.97
R3417:Kdm5b	UTSW	1	134,515,715 (GRCm39)	missense	probably damaging	1.00
R3771:Kdm5b	UTSW	1	134,541,083 (GRCm39)	missense	probably damaging	1.00
R3783:Kdm5b	UTSW	1	134,558,280 (GRCm39)	missense	probably benign
R3803:Kdm5b	UTSW	1	134,543,679 (GRCm39)	missense	probably benign	0.07
R3980:Kdm5b	UTSW	1	134,547,408 (GRCm39)	missense	probably benign	0.11
R3983:Kdm5b	UTSW	1	134,559,042 (GRCm39)	missense	possibly damaging	0.91
R4013:Kdm5b	UTSW	1	134,555,067 (GRCm39)	missense	possibly damaging	0.86
R4162:Kdm5b	UTSW	1	134,552,899 (GRCm39)	missense	probably benign	0.01
R4701:Kdm5b	UTSW	1	134,533,750 (GRCm39)	intron	probably benign
R4791:Kdm5b	UTSW	1	134,558,538 (GRCm39)	missense	possibly damaging	0.82
R4836:Kdm5b	UTSW	1	134,521,053 (GRCm39)	splice site	probably null
R4924:Kdm5b	UTSW	1	134,559,089 (GRCm39)	missense	probably benign	0.00
R5135:Kdm5b	UTSW	1	134,516,484 (GRCm39)	intron	probably benign
R5248:Kdm5b	UTSW	1	134,548,735 (GRCm39)	missense	probably benign	0.11
R5290:Kdm5b	UTSW	1	134,549,837 (GRCm39)	splice site	probably null
R5358:Kdm5b	UTSW	1	134,535,432 (GRCm39)	nonsense	probably null
R5388:Kdm5b	UTSW	1	134,536,635 (GRCm39)	nonsense	probably null
R5396:Kdm5b	UTSW	1	134,549,836 (GRCm39)	splice site	probably null
R5397:Kdm5b	UTSW	1	134,549,836 (GRCm39)	splice site	probably null
R5398:Kdm5b	UTSW	1	134,549,836 (GRCm39)	splice site	probably null
R5399:Kdm5b	UTSW	1	134,549,836 (GRCm39)	splice site	probably null
R5529:Kdm5b	UTSW	1	134,515,741 (GRCm39)	missense	probably damaging	1.00
R5540:Kdm5b	UTSW	1	134,558,979 (GRCm39)	missense	probably damaging	0.98
R5661:Kdm5b	UTSW	1	134,526,811 (GRCm39)	missense	probably benign	0.01
R5663:Kdm5b	UTSW	1	134,558,373 (GRCm39)	missense	probably benign
R5822:Kdm5b	UTSW	1	134,516,511 (GRCm39)	splice site	probably benign
R6226:Kdm5b	UTSW	1	134,536,616 (GRCm39)	missense	probably damaging	0.99
R6368:Kdm5b	UTSW	1	134,526,945 (GRCm39)	missense	probably damaging	1.00
R6681:Kdm5b	UTSW	1	134,541,007 (GRCm39)	missense	possibly damaging	0.90
R6715:Kdm5b	UTSW	1	134,536,799 (GRCm39)	critical splice donor site	probably null
R7132:Kdm5b	UTSW	1	134,526,844 (GRCm39)	missense	probably damaging	1.00
R7202:Kdm5b	UTSW	1	134,552,497 (GRCm39)	missense	probably benign
R7258:Kdm5b	UTSW	1	134,548,759 (GRCm39)	missense	probably damaging	1.00
R7335:Kdm5b	UTSW	1	134,488,177 (GRCm39)	missense	probably damaging	1.00
R7420:Kdm5b	UTSW	1	134,532,235 (GRCm39)	missense	probably benign	0.14
R7426:Kdm5b	UTSW	1	134,523,571 (GRCm39)	missense	probably benign	0.02
R7452:Kdm5b	UTSW	1	134,552,686 (GRCm39)	missense	probably damaging	1.00
R7595:Kdm5b	UTSW	1	134,536,704 (GRCm39)	missense	probably benign	0.00
R7612:Kdm5b	UTSW	1	134,552,656 (GRCm39)	nonsense	probably null
R7846:Kdm5b	UTSW	1	134,545,578 (GRCm39)	missense	probably damaging	1.00
R8115:Kdm5b	UTSW	1	134,547,411 (GRCm39)	missense	possibly damaging	0.83
R8146:Kdm5b	UTSW	1	134,552,864 (GRCm39)	missense	probably benign	0.05
R8160:Kdm5b	UTSW	1	134,541,657 (GRCm39)	missense	probably damaging	1.00
R8527:Kdm5b	UTSW	1	134,533,512 (GRCm39)	missense	possibly damaging	0.78
R8542:Kdm5b	UTSW	1	134,533,512 (GRCm39)	missense	possibly damaging	0.78
R8930:Kdm5b	UTSW	1	134,544,010 (GRCm39)	missense	probably damaging	1.00
R8932:Kdm5b	UTSW	1	134,544,010 (GRCm39)	missense	probably damaging	1.00
R8950:Kdm5b	UTSW	1	134,541,664 (GRCm39)	missense	possibly damaging	0.84
R9089:Kdm5b	UTSW	1	134,535,506 (GRCm39)	missense	probably damaging	0.98
R9109:Kdm5b	UTSW	1	134,528,493 (GRCm39)	critical splice donor site	probably null
R9133:Kdm5b	UTSW	1	134,530,323 (GRCm39)	missense	probably benign
R9298:Kdm5b	UTSW	1	134,528,493 (GRCm39)	critical splice donor site	probably null
R9423:Kdm5b	UTSW	1	134,515,705 (GRCm39)	missense	possibly damaging	0.85
R9630:Kdm5b	UTSW	1	134,512,971 (GRCm39)	critical splice donor site	probably null
R9670:Kdm5b	UTSW	1	134,558,240 (GRCm39)	nonsense	probably null
X0063:Kdm5b	UTSW	1	134,516,614 (GRCm39)	missense	probably benign	0.07
Z1176:Kdm5b	UTSW	1	134,552,773 (GRCm39)	missense	probably damaging	1.00
Z1177:Kdm5b	UTSW	1	134,523,536 (GRCm39)	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- CAACTTAGGCAAGCAAACACTTTTG -3'
(R):5'- AAGGACCCTTTGCAGTGAAAG -3'

Sequencing Primer
(F):5'- TGTTTTTAGTCTTAAGGGTGAAAAGG -3'
(R):5'- GACCCTTTGCAGTGAAAGATAAATTG -3'

Posted On

2019-11-12