Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02072:Kdm6a'

185866

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Kdm6a

Ensembl Gene

ENSMUSG00000037369

Gene Name

lysine (K)-specific demethylase 6A

Synonyms

Utx

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

IGL02072

Quality Score

Status

Chromosome

Chromosomal Location

18028814-18146175 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 18120528 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 737 (T737A)

Ref Sequence

ENSEMBL: ENSMUSP00000061539 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000044484] [ENSMUST00000052368] [ENSMUST00000223885] [ENSMUST00000224084] [ENSMUST00000224255]

AlphaFold

O70546

Predicted Effect

probably benign
Transcript: ENSMUST00000044484
AA Change: T737A

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000045862
Gene: ENSMUSG00000037369
AA Change: T737A

Domain	Start	End	E-Value	Type
low complexity region	9	19	N/A	INTRINSIC
low complexity region	28	42	N/A	INTRINSIC
TPR	95	128	4.2e-2	SMART
TPR	132	165	6.1e-6	SMART
TPR	207	240	3.3e-2	SMART
TPR	286	319	2.3e-3	SMART
TPR	320	353	2e-5	SMART
TPR	354	387	7.7e-2	SMART
low complexity region	814	833	N/A	INTRINSIC
low complexity region	919	932	N/A	INTRINSIC
low complexity region	972	983	N/A	INTRINSIC
low complexity region	1055	1071	N/A	INTRINSIC
JmjC	1095	1258	3.9e-51	SMART
Blast:JmjC	1294	1358	7e-35	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000052368
AA Change: T737A

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000061539
Gene: ENSMUSG00000037369
AA Change: T737A

Domain	Start	End	E-Value	Type
low complexity region	9	19	N/A	INTRINSIC
low complexity region	28	42	N/A	INTRINSIC
TPR	95	128	8.74e0	SMART
TPR	132	165	1.3e-3	SMART
TPR	207	240	7.01e0	SMART
TPR	286	319	4.69e-1	SMART
TPR	320	353	4.21e-3	SMART
TPR	354	387	1.6e1	SMART
low complexity region	814	833	N/A	INTRINSIC
low complexity region	919	932	N/A	INTRINSIC
low complexity region	972	983	N/A	INTRINSIC
low complexity region	1055	1071	N/A	INTRINSIC
JmjC	1095	1258	1.08e-48	SMART
Blast:JmjC	1294	1358	9e-35	BLAST

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130978

Predicted Effect

probably benign
Transcript: ENSMUST00000223885

Predicted Effect

probably benign
Transcript: ENSMUST00000224084

Predicted Effect

probably benign
Transcript: ENSMUST00000224255

Predicted Effect

unknown
Transcript: ENSMUST00000225336
AA Change: T332A

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000226046

Coding Region Coverage

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is located on the X chromosome and is the corresponding locus to a Y-linked gene which encodes a tetratricopeptide repeat (TPR) protein. The encoded protein of this gene contains a JmjC-domain and catalyzes the demethylation of tri/dimethylated histone H3. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Apr 2014]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality, caudal body truncation, abnormal neural tube closure and abnormal heart development. Mice hemizygous for this allele exhibit perinatal lethality, abnormal neural tube closure, inability to breath, exencephaly and atelectasis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 39 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930595D18Rik	T	A	12: 111,128,254 (GRCm39)		probably benign	Het
Atm	A	G	9: 53,371,096 (GRCm39)	S2251P	probably benign	Het
C1qtnf6	T	A	15: 78,411,551 (GRCm39)	K42*	probably null	Het
Ddx20	A	T	3: 105,587,943 (GRCm39)	V379E	probably damaging	Het
Dnah7a	A	T	1: 53,644,986 (GRCm39)	W1017R	probably damaging	Het
Eif2s1	T	A	12: 78,926,788 (GRCm39)	N179K	probably benign	Het
Exosc9	A	T	3: 36,608,821 (GRCm39)	N140I	probably damaging	Het
Fancg	A	C	4: 43,007,062 (GRCm39)	H238Q	probably benign	Het
Fyttd1	A	G	16: 32,721,031 (GRCm39)	I110V	probably damaging	Het
G6pd2	A	T	5: 61,966,753 (GRCm39)	D176V	probably damaging	Het
Gm5114	A	G	7: 39,060,826 (GRCm39)	S8P	probably benign	Het
Hoxa1	T	A	6: 52,133,878 (GRCm39)	M283L	probably damaging	Het
Hspbp1	A	T	7: 4,680,720 (GRCm39)	L252H	probably damaging	Het
Itgb2l	A	T	16: 96,231,808 (GRCm39)	D319E	probably benign	Het
Kmt2c	A	T	5: 25,610,430 (GRCm39)	D225E	possibly damaging	Het
Lamb2	T	A	9: 108,359,107 (GRCm39)	Y274*	probably null	Het
Lratd2	A	G	15: 60,695,302 (GRCm39)	L148P	probably damaging	Het
Mamdc4	A	G	2: 25,458,351 (GRCm39)	L353P	probably damaging	Het
Mid2	T	A	X: 139,637,201 (GRCm39)	H258Q	probably damaging	Het
Msh3	A	C	13: 92,436,803 (GRCm39)	N502K	probably damaging	Het
Nalcn	T	C	14: 123,560,770 (GRCm39)	H769R	probably benign	Het
Nfx1	A	G	4: 41,016,119 (GRCm39)	I894V	probably benign	Het
Notch3	G	A	17: 32,366,048 (GRCm39)	Q1018*	probably null	Het
Oas1e	A	G	5: 120,929,846 (GRCm39)		probably null	Het
Or4f14d	A	T	2: 111,960,426 (GRCm39)	H243Q	probably damaging	Het
Or7g34	A	G	9: 19,478,245 (GRCm39)	I145T	probably benign	Het
Plekha4	T	A	7: 45,187,722 (GRCm39)	F265I	probably benign	Het
Rnf123	G	A	9: 107,945,501 (GRCm39)	R390*	probably null	Het
Slc9a3	T	C	13: 74,313,978 (GRCm39)	I762T	probably benign	Het
Spag1	C	A	15: 36,190,658 (GRCm39)	P158Q	probably damaging	Het
Spout1	G	A	2: 30,067,938 (GRCm39)	Q26*	probably null	Het
Sulf1	T	C	1: 12,918,432 (GRCm39)	Y50H	probably damaging	Het
Sytl5	C	T	X: 9,829,825 (GRCm39)		probably benign	Het
Tcof1	T	C	18: 60,964,637 (GRCm39)	E663G	possibly damaging	Het
Tmc3	A	G	7: 83,265,148 (GRCm39)	I681V	probably benign	Het
Tnfsf4	G	T	1: 161,244,860 (GRCm39)	C183F	probably damaging	Het
Ubqln3	A	T	7: 103,790,506 (GRCm39)	L528Q	possibly damaging	Het
Upf3a	A	C	8: 13,848,368 (GRCm39)	Q388P	probably damaging	Het
Vrk1	T	C	12: 106,009,144 (GRCm39)	V70A	probably benign	Het

Other mutations in Kdm6a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00908:Kdm6a	APN	X	18,102,905 (GRCm39)	missense	possibly damaging	0.94
IGL00963:Kdm6a	APN	X	18,112,665 (GRCm39)	splice site	probably benign
IGL02426:Kdm6a	APN	X	18,112,549 (GRCm39)	missense	probably damaging	1.00
IGL03351:Kdm6a	APN	X	18,113,343 (GRCm39)	nonsense	probably null
R0539:Kdm6a	UTSW	X	18,128,664 (GRCm39)	missense	probably damaging	0.99
R1387:Kdm6a	UTSW	X	18,120,235 (GRCm39)	splice site	probably benign
R1809:Kdm6a	UTSW	X	18,102,923 (GRCm39)	missense	probably benign	0.44
R2238:Kdm6a	UTSW	X	18,065,476 (GRCm39)	missense	probably damaging	0.99
R2239:Kdm6a	UTSW	X	18,065,476 (GRCm39)	missense	probably damaging	0.99
R4062:Kdm6a	UTSW	X	18,117,114 (GRCm39)	missense	probably benign
R4063:Kdm6a	UTSW	X	18,117,114 (GRCm39)	missense	probably benign

Posted On

2014-05-07