Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL01553:Kdm1b'

90630

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Kdm1b

Ensembl Gene

ENSMUSG00000038080

Gene Name

lysine (K)-specific demethylase 1B

Synonyms

Aof1, 4632428N09Rik

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.406) question?

Stock #

IGL01553

Quality Score

Status

Chromosome

Chromosomal Location

47196849-47238085 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 47234024 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 786 (I786N)

Ref Sequence

ENSEMBL: ENSMUSP00000038373 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021807] [ENSMUST00000037025]

AlphaFold

Q8CIG3

Predicted Effect

probably benign
Transcript: ENSMUST00000021807

SMART Domains

Protein: ENSMUSP00000021807
Gene: ENSMUSG00000021377

Domain	Start	End	E-Value	Type
low complexity region	3	18	N/A	INTRINSIC
low complexity region	31	55	N/A	INTRINSIC
low complexity region	58	69	N/A	INTRINSIC
SAP	153	187	2.97e-8	SMART
low complexity region	190	210	N/A	INTRINSIC
low complexity region	231	315	N/A	INTRINSIC
Pfam:DEK_C	327	379	3.4e-19	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000037025
AA Change: I786N

PolyPhen 2 Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: I786N

Domain	Start	End	E-Value	Type
Pfam:zf-CW	138	191	2.6e-13	PFAM
low complexity region	235	253	N/A	INTRINSIC
Pfam:SWIRM	286	369	6e-12	PFAM
Pfam:Pyr_redox_2	368	490	3.1e-8	PFAM
Pfam:Thi4	375	446	2.2e-10	PFAM
Pfam:FAD_binding_3	388	423	4.1e-7	PFAM
Pfam:HI0933_like	389	428	1.6e-7	PFAM
Pfam:FAD_binding_2	390	428	1.6e-6	PFAM
Pfam:Pyr_redox	390	438	8e-8	PFAM
Pfam:NAD_binding_8	393	460	1.6e-13	PFAM
Pfam:Amino_oxidase	398	824	3.7e-86	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128977

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138401

Predicted Effect

unknown
Transcript: ENSMUST00000143518
AA Change: I402N

SMART Domains

Protein: ENSMUSP00000114999
Gene: ENSMUSG00000038080
AA Change: I402N

Domain	Start	End	E-Value	Type
Pfam:SWIRM	3	86	1.1e-12	PFAM
Pfam:Thi4	91	163	3.5e-10	PFAM
Pfam:FAD_binding_3	105	140	3.5e-7	PFAM
Pfam:HI0933_like	106	145	1.7e-7	PFAM
Pfam:Pyr_redox_2	106	251	1.5e-10	PFAM
Pfam:FAD_binding_2	107	150	5.7e-7	PFAM
Pfam:Pyr_redox	107	158	6.4e-8	PFAM
Pfam:Pyr_redox_3	109	288	1.2e-13	PFAM
Pfam:NAD_binding_8	110	177	2.3e-13	PFAM
Pfam:Amino_oxidase	115	181	8.6e-19	PFAM
Pfam:Amino_oxidase	178	441	4.5e-63	PFAM

Coding Region Coverage

Validation Efficiency

MGI Phenotype

PHENOTYPE: Homozygous null mice of both sexes are viable, grossly normal and male mice are fertile; however, heterozygous progeny of homozygous null mothers display severe placental defects, embryonic growth impairment, neural tube defects and pericardial edema, and do not survive past E10.5. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 26 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Akr1c13	T	A	13: 4,244,774 (GRCm39)	H117Q	probably damaging	Het
Arhgap44	T	C	11: 64,943,944 (GRCm39)	N188S	probably damaging	Het
Bach1	T	A	16: 87,519,393 (GRCm39)	I561N	probably damaging	Het
Bsph2	G	T	7: 13,290,645 (GRCm39)	T78K	probably damaging	Het
Ccdc178	A	G	18: 22,048,063 (GRCm39)	Y776H	probably damaging	Het
Ccdc7a	T	C	8: 129,753,072 (GRCm39)		probably benign	Het
Cenpp	C	T	13: 49,618,252 (GRCm39)	V218M	probably damaging	Het
Dnmt3l	A	G	10: 77,899,082 (GRCm39)	S94G	probably benign	Het
Dock7	A	T	4: 98,833,803 (GRCm39)	Y1839*	probably null	Het
Gabra6	T	A	11: 42,206,023 (GRCm39)	T278S	probably damaging	Het
Galnt11	G	A	5: 25,452,718 (GRCm39)	D77N	probably benign	Het
Gm17175	T	C	14: 51,808,279 (GRCm39)	D171G	probably benign	Het
Iqch	T	C	9: 63,408,199 (GRCm39)	N655S	probably benign	Het
Macf1	G	A	4: 123,386,956 (GRCm39)	Q976*	probably null	Het
Mbtd1	T	A	11: 93,814,040 (GRCm39)	C228S	probably benign	Het
Myo10	T	C	15: 25,776,415 (GRCm39)	L46P	probably damaging	Het
Niban3	G	T	8: 72,055,546 (GRCm39)	A319S	possibly damaging	Het
Nup133	A	G	8: 124,642,063 (GRCm39)	V800A	possibly damaging	Het
Or5h23	G	T	16: 58,906,685 (GRCm39)	H54N	probably benign	Het
Prkca	C	T	11: 107,948,660 (GRCm39)	G110R	probably benign	Het
Samd9l	A	T	6: 3,375,566 (GRCm39)	M565K	probably damaging	Het
Scgn	T	C	13: 24,143,662 (GRCm39)	Q77R	probably benign	Het
Serpinb6b	T	C	13: 33,158,931 (GRCm39)	L44P	probably damaging	Het
Tfrc	T	C	16: 32,447,403 (GRCm39)	V673A	probably benign	Het
Tsfm	G	A	10: 126,864,259 (GRCm39)	T152M	probably benign	Het
Wdfy3	A	T	5: 102,047,897 (GRCm39)	C1803S	probably benign	Het

Other mutations in Kdm1b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00587:Kdm1b	APN	13	47,222,016 (GRCm39)	missense	probably benign	0.01
IGL00924:Kdm1b	APN	13	47,221,956 (GRCm39)	missense	probably benign
IGL01663:Kdm1b	APN	13	47,227,213 (GRCm39)	missense	probably damaging	0.99
IGL02385:Kdm1b	APN	13	47,221,982 (GRCm39)	missense	possibly damaging	0.49
IGL02505:Kdm1b	APN	13	47,214,331 (GRCm39)	missense	probably damaging	1.00
IGL02826:Kdm1b	APN	13	47,233,943 (GRCm39)	missense	probably damaging	1.00
IGL03257:Kdm1b	APN	13	47,202,742 (GRCm39)	missense	probably damaging	1.00
R0052:Kdm1b	UTSW	13	47,217,593 (GRCm39)	missense	probably damaging	1.00
R0319:Kdm1b	UTSW	13	47,207,195 (GRCm39)	missense	probably benign
R0426:Kdm1b	UTSW	13	47,217,720 (GRCm39)	splice site	probably benign
R0599:Kdm1b	UTSW	13	47,212,286 (GRCm39)	missense	possibly damaging	0.47
R0764:Kdm1b	UTSW	13	47,222,079 (GRCm39)	missense	possibly damaging	0.70
R1163:Kdm1b	UTSW	13	47,225,398 (GRCm39)	missense	probably benign	0.02
R1543:Kdm1b	UTSW	13	47,221,997 (GRCm39)	missense	probably damaging	0.99
R1584:Kdm1b	UTSW	13	47,217,530 (GRCm39)	missense	probably damaging	1.00
R1627:Kdm1b	UTSW	13	47,217,707 (GRCm39)	critical splice donor site	probably null
R1669:Kdm1b	UTSW	13	47,222,024 (GRCm39)	missense	probably damaging	1.00
R1758:Kdm1b	UTSW	13	47,214,244 (GRCm39)	missense	probably benign	0.00
R1860:Kdm1b	UTSW	13	47,202,666 (GRCm39)	missense	probably benign	0.03
R1907:Kdm1b	UTSW	13	47,217,596 (GRCm39)	missense	probably benign	0.00
R2225:Kdm1b	UTSW	13	47,217,564 (GRCm39)	frame shift	probably null
R2239:Kdm1b	UTSW	13	47,227,231 (GRCm39)	missense	probably damaging	1.00
R2271:Kdm1b	UTSW	13	47,217,564 (GRCm39)	frame shift	probably null
R2302:Kdm1b	UTSW	13	47,217,564 (GRCm39)	frame shift	probably null
R2303:Kdm1b	UTSW	13	47,217,564 (GRCm39)	frame shift	probably null
R2380:Kdm1b	UTSW	13	47,227,231 (GRCm39)	missense	probably damaging	1.00
R2442:Kdm1b	UTSW	13	47,216,451 (GRCm39)	missense	probably benign	0.32
R3022:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R3054:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R3545:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R3546:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R3548:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R4094:Kdm1b	UTSW	13	47,216,496 (GRCm39)	missense	probably damaging	1.00
R4419:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R4420:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R4502:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R4547:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R4548:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R4785:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R4793:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R4804:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R4882:Kdm1b	UTSW	13	47,214,369 (GRCm39)	missense	probably benign
R4906:Kdm1b	UTSW	13	47,216,620 (GRCm39)	critical splice donor site	probably null
R4965:Kdm1b	UTSW	13	47,227,843 (GRCm39)	missense	probably damaging	0.98
R5039:Kdm1b	UTSW	13	47,230,962 (GRCm39)	missense	probably damaging	1.00
R5098:Kdm1b	UTSW	13	47,216,467 (GRCm39)	missense	probably damaging	1.00
R5265:Kdm1b	UTSW	13	47,216,445 (GRCm39)	missense	probably benign	0.35
R5541:Kdm1b	UTSW	13	47,232,672 (GRCm39)	missense	probably damaging	1.00
R5814:Kdm1b	UTSW	13	47,216,622 (GRCm39)	splice site	probably null
R6046:Kdm1b	UTSW	13	47,232,729 (GRCm39)	missense	possibly damaging	0.92
R6798:Kdm1b	UTSW	13	47,222,012 (GRCm39)	missense	probably benign	0.00
R6903:Kdm1b	UTSW	13	47,227,880 (GRCm39)	missense	probably benign	0.00
R7831:Kdm1b	UTSW	13	47,204,098 (GRCm39)	missense	probably benign	0.17
R7973:Kdm1b	UTSW	13	47,230,922 (GRCm39)	missense	probably benign	0.00
R8181:Kdm1b	UTSW	13	47,205,377 (GRCm39)	critical splice donor site	probably null
R8248:Kdm1b	UTSW	13	47,225,354 (GRCm39)	intron	probably benign
R8821:Kdm1b	UTSW	13	47,217,617 (GRCm39)	missense	possibly damaging	0.94
R8831:Kdm1b	UTSW	13	47,217,617 (GRCm39)	missense	possibly damaging	0.94
R8842:Kdm1b	UTSW	13	47,231,832 (GRCm39)	missense	probably damaging	1.00
R8861:Kdm1b	UTSW	13	47,217,582 (GRCm39)	missense	probably benign	0.02
R8885:Kdm1b	UTSW	13	47,207,184 (GRCm39)	nonsense	probably null
R9038:Kdm1b	UTSW	13	47,202,770 (GRCm39)	missense	probably benign	0.07
R9132:Kdm1b	UTSW	13	47,225,458 (GRCm39)	missense	probably benign	0.05
R9268:Kdm1b	UTSW	13	47,217,705 (GRCm39)	missense	probably benign	0.00
R9616:Kdm1b	UTSW	13	47,234,030 (GRCm39)	missense	probably damaging	1.00

Posted On

2013-12-09