Mutagenetix > Incidental Mutation

Incidental Mutation 'PIT4486001:Kdm5b'

556084

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

Accession Numbers

Essential gene?

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

Stock #

PIT4486001 (G1)

Quality Score

184.009

Status

Not validated

Chromosome

Chromosomal Location

134487916-134560621 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 134556423 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Glutamine at position 1370 (L1370Q)

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: L1370Q

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

SMART Domains

Protein: ENSMUSP00000038138
Gene: ENSMUSG00000042207
AA Change: L1370Q

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: L1370Q

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

SMART Domains

Protein: ENSMUSP00000107817
Gene: ENSMUSG00000042207
AA Change: L1370Q

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: 93.0%
3x: 90.5%
10x: 84.1%
20x: 70.1%

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: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700018F24Rik	T	C	5: 144,980,914 (GRCm39)	S108P	probably damaging	Het
Abhd16b	A	T	2: 181,135,752 (GRCm39)	Q218L	probably benign	Het
Abhd3	T	A	18: 10,645,233 (GRCm39)	I354F	probably benign	Het
Abt1	T	C	13: 23,607,851 (GRCm39)	Y51C	possibly damaging	Het
Actl9	T	A	17: 33,653,172 (GRCm39)	Y411N	possibly damaging	Het
Ano4	A	G	10: 88,828,891 (GRCm39)	V516A	probably damaging	Het
Bptf	A	T	11: 106,945,614 (GRCm39)	S2542T	probably damaging	Het
Card11	C	T	5: 140,862,163 (GRCm39)	V1045M	probably damaging	Het
Ccdc121	T	A	5: 31,645,087 (GRCm39)	I280K	probably damaging	Het
Cd300ld2	CGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGTCAGAACTGTGGATGGCACAACTGTGCATGGCAGAACTGTGGATGGCACAACTGTGGATGGCAGAACTGTGG	CGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGGCAGAACTGTGGATGTCAGAACTGTGGATGTCAGAACTGTGGATGGCACAACTGTGCATGGCAGAACTGTGGATGGCACAACTGTGGATGGCAGAACTGTGG	11: 114,903,257 (GRCm39)		probably benign	Het
Cdh3	A	G	8: 107,268,122 (GRCm39)	K386E	possibly damaging	Het
Cks1b	C	A	3: 89,323,621 (GRCm39)	Q49H	probably damaging	Het
Clpb	A	T	7: 101,313,139 (GRCm39)	D41V	probably benign	Het
Cyp3a11	A	T	5: 145,797,302 (GRCm39)	M359K	probably damaging	Het
Cyp3a13	A	T	5: 137,908,228 (GRCm39)	I207N	probably benign	Het
Dennd4c	T	A	4: 86,717,701 (GRCm39)	L566*	probably null	Het
Dhtkd1	A	T	2: 5,904,806 (GRCm39)	D859E	probably benign	Het
Efcab6	T	C	15: 83,857,514 (GRCm39)	D295G	probably benign	Het
Fcgbp	A	G	7: 27,774,698 (GRCm39)	T91A	possibly damaging	Het
Gm11569	GCAGCTGGGCCTGCAGCAGCTGGAAATGCAGCAGCTAGGACGGCAACA	GCA	11: 99,689,491 (GRCm39)		probably benign	Het
Gsdma3	A	G	11: 98,528,880 (GRCm39)	K454E	unknown	Het
Herc1	T	A	9: 66,279,671 (GRCm39)	I193N	probably damaging	Het
Lrrc37	A	T	11: 103,509,027 (GRCm39)	H980Q	unknown	Het
Map4	T	G	9: 109,901,682 (GRCm39)	V965G	probably damaging	Het
Mkrn2os	T	C	6: 115,562,444 (GRCm39)	D173G	probably benign	Het
Ndfip2	A	G	14: 105,532,300 (GRCm39)	D232G	probably damaging	Het
Nipal2	C	T	15: 34,584,875 (GRCm39)	G231D	probably damaging	Het
Notch3	A	T	17: 32,373,737 (GRCm39)	N490K	probably damaging	Het
Or5p68	A	G	7: 107,945,529 (GRCm39)	S220P	possibly damaging	Het
Or8g50	T	A	9: 39,648,535 (GRCm39)	C141*	probably null	Het
Prkar2a	T	C	9: 108,610,326 (GRCm39)	L185S	probably damaging	Het
Ptpn9	T	G	9: 56,968,287 (GRCm39)	N542K	probably damaging	Het
Pus10	G	A	11: 23,662,326 (GRCm39)		probably null	Het
Pyroxd2	A	G	19: 42,728,828 (GRCm39)	S191P	probably benign	Het
Rab15	T	A	12: 76,848,716 (GRCm39)	K122*	probably null	Het
Rara	A	G	11: 98,864,321 (GRCm39)	N416S	possibly damaging	Het
Rims2	T	C	15: 39,339,916 (GRCm39)	V870A	possibly damaging	Het
Sec16a	T	C	2: 26,315,785 (GRCm39)	T293A		Het
Slc26a3	G	A	12: 31,520,949 (GRCm39)	D718N	probably benign	Het
Slc44a5	G	A	3: 153,964,659 (GRCm39)	V520I	possibly damaging	Het
Spata31e2	G	A	1: 26,724,410 (GRCm39)	P257S	probably damaging	Het
Tgfb2	A	T	1: 186,422,924 (GRCm39)	Y142N	probably benign	Het
Tgfbi	A	T	13: 56,777,607 (GRCm39)	I364F	probably damaging	Het
Tmem144	A	C	3: 79,734,174 (GRCm39)	D176E	probably benign	Het
Tns4	A	T	11: 98,962,161 (GRCm39)	L612Q	probably damaging	Het
Toe1	A	G	4: 116,663,692 (GRCm39)	L76S	probably damaging	Het
Trank1	T	C	9: 111,219,175 (GRCm39)	F1971L	probably damaging	Het
Tsen54	G	T	11: 115,713,422 (GRCm39)	V481F	probably damaging	Het
Uimc1	A	G	13: 55,223,381 (GRCm39)	L297P	probably damaging	Het
Wnt8a	T	C	18: 34,680,636 (GRCm39)	Y334H	probably damaging	Het
Zfp281	A	G	1: 136,554,741 (GRCm39)	D573G	possibly damaging	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
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
R7704:Kdm5b	UTSW	1	134,515,669 (GRCm39)	missense	probably damaging	1.00
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'- AATCTGCGTTAGCCCTGCTC -3'
(R):5'- CAGACAGTTTGTGTGCTCTCG -3'

Sequencing Primer
(F):5'- CTCTGGTTTAGGGGCATTAAGAC -3'
(R):5'- TGCTCTCGTGGCTCAAAGAC -3'

Posted On

2019-06-07