Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL00959:Jmjd6'

28598

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Jmjd6

Ensembl Gene

ENSMUSG00000056962

Gene Name

jumonji domain containing 6

Synonyms

5730436I23Rik, Ptdsr, PSR, PtdSerR

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

IGL00959

Quality Score

Status

Chromosome

Chromosomal Location

116728258-116734275 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 116733202 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 115 (D115E)

Ref Sequence

ENSEMBL: ENSMUSP00000115086 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047616] [ENSMUST00000106370] [ENSMUST00000140349] [ENSMUST00000140513] [ENSMUST00000142495]

AlphaFold

Q9ERI5

Predicted Effect

probably benign
Transcript: ENSMUST00000047616
AA Change: D158E

PolyPhen 2 Score 0.416 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000047570
Gene: ENSMUSG00000056962
AA Change: D158E

Domain	Start	End	E-Value	Type
JmjC	141	305	6.09e-48	SMART
low complexity region	340	369	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000106370

SMART Domains

Protein: ENSMUSP00000101978
Gene: ENSMUSG00000090266

Domain	Start	End	E-Value	Type
low complexity region	5	22	N/A	INTRINSIC
Pfam:Methyltransf_16	48	203	9.9e-20	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000124831

SMART Domains

Protein: ENSMUSP00000122867
Gene: ENSMUSG00000056962

Domain	Start	End	E-Value	Type
Pfam:JmjC	1	81	6.3e-20	PFAM
low complexity region	150	179	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128784

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130120

Predicted Effect

probably benign
Transcript: ENSMUST00000132593

Predicted Effect

probably benign
Transcript: ENSMUST00000140349
AA Change: D110E

PolyPhen 2 Score 0.051 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000120850
Gene: ENSMUSG00000056962
AA Change: D110E

Domain	Start	End	E-Value	Type
JmjC	93	257	6.09e-48	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000140513
AA Change: D115E

PolyPhen 2 Score 0.683 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000115086
Gene: ENSMUSG00000056962
AA Change: D115E

Domain	Start	End	E-Value	Type
JmjC	98	262	6.09e-48	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000142495
AA Change: D158E

PolyPhen 2 Score 0.260 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000117922
Gene: ENSMUSG00000056962
AA Change: D158E

Domain	Start	End	E-Value	Type
JmjC	141	270	4.17e-14	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176765

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176799

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184052

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141735

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175930

Predicted Effect

probably benign
Transcript: ENSMUST00000140869

Coding Region Coverage

Validation Efficiency

MGI Phenotype

FUNCTION: This gene encodes a nuclear protein with a JmjC domain. JmjC domain-containing proteins are predicted to function as protein hydroxylases or histone demethylases. This protein functions in differentiation of multiple tissues during development, and in anti-inflammatory cytokine signaling. It was first identified as a putative phosphatidylserine receptor involved in phagocytosis of apoptotic cells; however, subsequent studies have indicated that this protein does not directly function in the clearance of apoptotic cells, and questioned whether it is a true phosphatidylserine receptor. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for disruptions in this gene show perinatal lethality. Abnormalities are observed in the nervous. respiratory, cardiovascular, digestive, renal, hematopoietic, and immune systems. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 37 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Alox12b	A	T	11: 69,057,069 (GRCm39)	H430L	probably damaging	Het
Aox4	G	T	1: 58,278,333 (GRCm39)	V443F	probably damaging	Het
Bmpr2	A	T	1: 59,854,474 (GRCm39)	I108F	possibly damaging	Het
Cflar	G	A	1: 58,768,321 (GRCm39)		probably null	Het
Chchd3	A	G	6: 32,945,188 (GRCm39)	V106A	probably benign	Het
Chl1	G	T	6: 103,686,211 (GRCm39)		probably null	Het
Clvs2	C	T	10: 33,404,459 (GRCm39)	M252I	probably benign	Het
Cntnap5a	T	A	1: 116,112,057 (GRCm39)	L449Q	probably benign	Het
Col6a2	T	A	10: 76,450,368 (GRCm39)	I188F	probably damaging	Het
Cyp2c55	A	G	19: 39,026,587 (GRCm39)	D398G	probably benign	Het
Dennd1b	T	C	1: 139,071,626 (GRCm39)		probably benign	Het
Dop1a	T	A	9: 86,369,484 (GRCm39)	Y106N	probably damaging	Het
Dpy19l1	A	T	9: 24,334,493 (GRCm39)		probably null	Het
Extl3	C	T	14: 65,314,361 (GRCm39)	V274I	probably benign	Het
Fras1	G	A	5: 96,929,140 (GRCm39)	R3848H	probably damaging	Het
Gm11437	A	C	11: 84,039,448 (GRCm39)		probably benign	Het
Gss	T	A	2: 155,423,871 (GRCm39)	D2V	probably damaging	Het
Hnrnpm	C	A	17: 33,868,876 (GRCm39)	R517L	probably damaging	Het
Ilvbl	G	A	10: 78,419,739 (GRCm39)	D548N	probably damaging	Het
Kidins220	T	A	12: 25,101,132 (GRCm39)	S1110R	possibly damaging	Het
Kmt2c	T	A	5: 25,481,227 (GRCm39)	I4784F	probably damaging	Het
Mrpl52	T	C	14: 54,664,494 (GRCm39)	V11A	possibly damaging	Het
Myo3b	A	G	2: 70,144,636 (GRCm39)	Y1036C	probably damaging	Het
Omp	T	C	7: 97,794,357 (GRCm39)	D90G	probably damaging	Het
Or6c2b	T	A	10: 128,947,893 (GRCm39)	M134L	probably benign	Het
Osmr	T	C	15: 6,854,086 (GRCm39)	I541V	probably benign	Het
Ppp2r1a	A	T	17: 21,181,840 (GRCm39)		probably benign	Het
Ptpn13	T	A	5: 103,665,437 (GRCm39)		probably null	Het
Rock2	C	A	12: 17,028,056 (GRCm39)	N1429K	probably benign	Het
Saxo4	A	T	19: 10,454,887 (GRCm39)		probably null	Het
Slc25a20	T	G	9: 108,559,198 (GRCm39)	M188R	possibly damaging	Het
Slc28a1	T	C	7: 80,818,816 (GRCm39)		probably benign	Het
Sult2a6	T	C	7: 13,988,634 (GRCm39)	Y42C	probably damaging	Het
Tgfb2	A	G	1: 186,436,784 (GRCm39)	V63A	probably benign	Het
Ugt2b38	A	T	5: 87,559,682 (GRCm39)	N403K	probably damaging	Het
Vmn2r29	A	G	7: 7,244,855 (GRCm39)	W340R	probably benign	Het
Wnt5a	C	T	14: 28,244,866 (GRCm39)	T351M	probably damaging	Het

Other mutations in Jmjd6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01877:Jmjd6	APN	11	116,733,519 (GRCm39)	missense	probably benign
IGL01941:Jmjd6	APN	11	116,732,184 (GRCm39)	splice site	probably null
IGL02316:Jmjd6	APN	11	116,733,928 (GRCm39)	missense	possibly damaging	0.50
IGL03396:Jmjd6	APN	11	116,732,077 (GRCm39)	missense	probably damaging	1.00
jumanji	UTSW	11	116,733,326 (GRCm39)	missense	probably damaging	1.00
R0675:Jmjd6	UTSW	11	116,731,353 (GRCm39)	missense	probably damaging	1.00
R1531:Jmjd6	UTSW	11	116,733,266 (GRCm39)	missense	probably benign
R2259:Jmjd6	UTSW	11	116,732,140 (GRCm39)	missense	probably damaging	1.00
R3937:Jmjd6	UTSW	11	116,731,991 (GRCm39)	missense	probably benign
R4284:Jmjd6	UTSW	11	116,733,534 (GRCm39)	missense	probably damaging	1.00
R5534:Jmjd6	UTSW	11	116,731,252 (GRCm39)	missense	probably damaging	1.00
R5881:Jmjd6	UTSW	11	116,730,682 (GRCm39)	nonsense	probably null
R6546:Jmjd6	UTSW	11	116,733,326 (GRCm39)	missense	probably damaging	1.00
R7468:Jmjd6	UTSW	11	116,733,275 (GRCm39)	missense	probably damaging	1.00
R7940:Jmjd6	UTSW	11	116,734,055 (GRCm39)	start gained	probably benign
R9370:Jmjd6	UTSW	11	116,729,952 (GRCm39)	missense	probably benign	0.00
R9790:Jmjd6	UTSW	11	116,733,438 (GRCm39)	missense	probably benign
R9791:Jmjd6	UTSW	11	116,733,438 (GRCm39)	missense	probably benign

Posted On

2013-04-17