Mutagenetix > Incidental Mutation

Incidental Mutation 'R0675:Jmjd6'

61621

Institutional Source

Beutler Lab

Gene Symbol

Jmjd6

Ensembl Gene

ENSMUSG00000056962

Gene Name

jumonji domain containing 6

Synonyms

5730436I23Rik, Ptdsr, PSR, PtdSerR

MMRRC Submission

038860-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0675 (G1)

Quality Score

142

Status

Validated

Chromosome

Chromosomal Location

116728258-116734275 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 116731353 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 232 (V232A)

Ref Sequence

ENSEMBL: ENSMUSP00000115086 (fasta)

Gene Model

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

AlphaFold

Q9ERI5

Predicted Effect

probably damaging
Transcript: ENSMUST00000047616
AA Change: V275A

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

SMART Domains

Protein: ENSMUSP00000047570
Gene: ENSMUSG00000056962
AA Change: V275A

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

possibly damaging
Transcript: ENSMUST00000124831
AA Change: V67A

PolyPhen 2 Score 0.949 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000122867
Gene: ENSMUSG00000056962
AA Change: V67A

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 damaging
Transcript: ENSMUST00000140349
AA Change: V227A

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

SMART Domains

Protein: ENSMUSP00000120850
Gene: ENSMUSG00000056962
AA Change: V227A

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000140513
AA Change: V232A

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

SMART Domains

Protein: ENSMUSP00000115086
Gene: ENSMUSG00000056962
AA Change: V232A

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141735

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175930

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176765

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176799

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184052

Predicted Effect

probably benign
Transcript: ENSMUST00000140869

Predicted Effect

probably benign
Transcript: ENSMUST00000142495

SMART Domains

Protein: ENSMUSP00000117922
Gene: ENSMUSG00000056962

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

Meta Mutation Damage Score

0.8489

Coding Region Coverage

1x: 99.4%
3x: 98.9%
10x: 97.7%
20x: 96.1%

Validation Efficiency

97% (88/91)

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: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ablim2	C	T	5: 36,024,124 (GRCm39)		probably benign	Het
Aire	T	C	10: 77,870,327 (GRCm39)		probably benign	Het
Akap12	T	C	10: 4,303,315 (GRCm39)	S42P	probably benign	Het
Amigo1	T	C	3: 108,098,985 (GRCm39)		probably benign	Het
Angptl3	A	G	4: 98,921,499 (GRCm39)	T206A	probably benign	Het
Ank1	T	A	8: 23,600,400 (GRCm39)		probably benign	Het
Ano5	A	T	7: 51,224,558 (GRCm39)	T472S	probably damaging	Het
Arid3c	T	C	4: 41,725,958 (GRCm39)	D215G	probably damaging	Het
Cd200	T	C	16: 45,217,473 (GRCm39)	I73V	probably benign	Het
Cd47	T	C	16: 49,727,162 (GRCm39)	I318T	possibly damaging	Het
Cep290	A	G	10: 100,404,675 (GRCm39)		probably null	Het
Cep350	A	G	1: 155,835,499 (GRCm39)	S66P	possibly damaging	Het
Cfap46	C	T	7: 139,255,950 (GRCm39)	C300Y	probably damaging	Het
Chd1	T	A	17: 15,978,523 (GRCm39)		probably benign	Het
Chd5	C	A	4: 152,470,407 (GRCm39)	T1913K	probably benign	Het
Cimip3	T	C	17: 47,724,701 (GRCm39)	E140G	probably benign	Het
Clec4b1	A	G	6: 123,048,405 (GRCm39)	Y180C	probably damaging	Het
Cntnap5c	A	T	17: 58,341,990 (GRCm39)	D227V	probably damaging	Het
Col19a1	C	G	1: 24,614,536 (GRCm39)		probably benign	Het
Csmd1	A	T	8: 16,208,145 (GRCm39)	M1270K	probably benign	Het
Cyp2c66	T	A	19: 39,175,060 (GRCm39)	F487I	possibly damaging	Het
Dpp8	T	C	9: 64,973,784 (GRCm39)		probably benign	Het
Duoxa1	A	T	2: 122,136,861 (GRCm39)		probably benign	Het
Edil3	A	G	13: 89,325,399 (GRCm39)	K263E	probably damaging	Het
Fat2	A	G	11: 55,200,035 (GRCm39)	L1013P	probably damaging	Het
Fras1	T	C	5: 96,815,246 (GRCm39)		probably benign	Het
Gab1	A	G	8: 81,496,297 (GRCm39)	S668P	probably damaging	Het
Galnt14	T	C	17: 73,852,030 (GRCm39)	T130A	probably damaging	Het
Gm10192	G	A	4: 97,071,109 (GRCm39)	H99Y	unknown	Het
Gm5592	A	G	7: 40,938,811 (GRCm39)	T698A	possibly damaging	Het
Gm6605	C	A	7: 38,147,699 (GRCm39)		noncoding transcript	Het
Gsdma3	A	G	11: 98,522,017 (GRCm39)	K149R	probably benign	Het
Igkv4-71	A	G	6: 69,220,411 (GRCm39)	S29P	probably damaging	Het
Igsf10	C	T	3: 59,236,015 (GRCm39)	V1389I	probably benign	Het
Ik	T	C	18: 36,880,386 (GRCm39)		probably benign	Het
Ino80	G	A	2: 119,213,962 (GRCm39)	P1203S	probably damaging	Het
Iqsec2	G	A	X: 150,987,120 (GRCm39)	E398K	possibly damaging	Het
Klhdc9	G	A	1: 171,187,895 (GRCm39)	T112M	possibly damaging	Het
Marcks	A	G	10: 37,017,181 (GRCm39)		probably benign	Het
Mctp2	T	A	7: 71,732,918 (GRCm39)	T829S	probably damaging	Het
Mroh2a	C	A	1: 88,156,102 (GRCm39)	A78E	probably damaging	Het
Mroh2a	G	A	1: 88,178,064 (GRCm39)	D1053N	probably damaging	Het
Mtmr14	A	T	6: 113,247,608 (GRCm39)	H518L	probably damaging	Het
Myo5c	T	C	9: 75,185,571 (GRCm39)	M978T	probably benign	Het
Nlrc3	T	C	16: 3,766,775 (GRCm39)	I1015V	probably benign	Het
Nlrp5	C	A	7: 23,116,842 (GRCm39)	Q189K	possibly damaging	Het
Or1e26	A	C	11: 73,480,078 (GRCm39)	L162R	probably damaging	Het
Or2h2c	G	C	17: 37,422,347 (GRCm39)	L176V	probably benign	Het
Or51f1d	A	G	7: 102,700,909 (GRCm39)	I135V	probably benign	Het
Or8k35	T	C	2: 86,424,423 (GRCm39)	I250V	probably benign	Het
Otof	T	A	5: 30,539,705 (GRCm39)	Y1051F	probably benign	Het
Pcdhb14	C	A	18: 37,581,392 (GRCm39)	T166K	possibly damaging	Het
Pla2g4e	A	G	2: 120,030,679 (GRCm39)		probably benign	Het
Polr3gl	T	C	3: 96,489,471 (GRCm39)	E20G	probably damaging	Het
Psmd1	A	G	1: 86,009,761 (GRCm39)	D295G	probably benign	Het
Ptpn21	C	A	12: 98,654,475 (GRCm39)	A831S	probably benign	Het
Pwwp3a	T	A	10: 80,065,914 (GRCm39)	V56E	probably damaging	Het
Rd3l	T	C	12: 111,946,596 (GRCm39)	D60G	probably benign	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Rnf213	A	G	11: 119,332,660 (GRCm39)	D2624G	probably benign	Het
Sec31a	T	C	5: 100,541,066 (GRCm39)	D347G	probably damaging	Het
Sema4g	G	A	19: 44,986,026 (GRCm39)	R289H	probably damaging	Het
Sema5b	C	T	16: 35,480,703 (GRCm39)	T761I	probably benign	Het
Septin1	A	T	7: 126,816,171 (GRCm39)	F86L	probably damaging	Het
Shank3	T	C	15: 89,415,591 (GRCm39)	V627A	possibly damaging	Het
Slc25a46	C	A	18: 31,742,641 (GRCm39)	G75V	probably benign	Het
Slc45a2	T	A	15: 11,025,864 (GRCm39)	Y405N	probably damaging	Het
Spidr	T	C	16: 15,855,498 (GRCm39)	E339G	probably damaging	Het
Sptbn1	A	T	11: 30,067,903 (GRCm39)	H1770Q	probably damaging	Het
Srgap1	T	C	10: 121,628,140 (GRCm39)	Y944C	probably damaging	Het
Supt20	C	T	3: 54,614,390 (GRCm39)	T169I	probably damaging	Het
Tie1	G	A	4: 118,336,966 (GRCm39)	Q587*	probably null	Het
Tmem214	A	G	5: 31,029,169 (GRCm39)	T203A	possibly damaging	Het
Tmprss15	C	A	16: 78,782,838 (GRCm39)	S742I	probably damaging	Het
Wdr87-ps	T	C	7: 29,231,942 (GRCm39)		noncoding transcript	Het
Zfhx2	A	G	14: 55,300,620 (GRCm39)	V2377A	probably damaging	Het
Zfp763	G	A	17: 33,238,774 (GRCm39)	H124Y	possibly damaging	Het
Zfp846	T	C	9: 20,504,853 (GRCm39)	S238P	probably benign	Het

Other mutations in Jmjd6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00959:Jmjd6	APN	11	116,733,202 (GRCm39)	missense	possibly damaging	0.68
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
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

Predicted Primers

PCR Primer
(F):5'- TTTCTACCCACAGGTCGGTAAGGC -3'
(R):5'- CAGCAGTGAGAGTTTCAAGGCTAGG -3'

Sequencing Primer
(F):5'- ACATGGCAGCAGGGACC -3'
(R):5'- GGGTCCTCCTAGAACCTTTG -3'

Posted On

2013-07-30