Mutagenetix > Incidental Mutation

Incidental Mutation 'R6546:Jmjd6'

521216

Institutional Source

Beutler Lab

Gene Symbol

Jmjd6

Ensembl Gene

ENSMUSG00000056962

Gene Name

jumonji domain containing 6

Synonyms

5730436I23Rik, Ptdsr, PSR, PtdSerR

MMRRC Submission

045325-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6546 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

116728258-116734275 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 116733326 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 117 (Y117C)

Ref Sequence

ENSEMBL: ENSMUSP00000117922 (fasta)

Gene Model

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

AlphaFold

Q9ERI5

Predicted Effect

probably damaging
Transcript: ENSMUST00000047616
AA Change: Y117C

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

SMART Domains

Protein: ENSMUSP00000047570
Gene: ENSMUSG00000056962
AA Change: Y117C

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 damaging
Transcript: ENSMUST00000140349
AA Change: Y69C

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

SMART Domains

Protein: ENSMUSP00000120850
Gene: ENSMUSG00000056962
AA Change: Y69C

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000140513
AA Change: Y74C

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

SMART Domains

Protein: ENSMUSP00000115086
Gene: ENSMUSG00000056962
AA Change: Y74C

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000142495
AA Change: Y117C

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

SMART Domains

Protein: ENSMUSP00000117922
Gene: ENSMUSG00000056962
AA Change: Y117C

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184052

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

probably benign
Transcript: ENSMUST00000140869

Meta Mutation Damage Score

0.9374

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.3%
20x: 97.6%

Validation Efficiency

100% (35/35)

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: 34 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Agbl3	T	A	6: 34,776,234 (GRCm39)	L242M	probably damaging	Het
Atad2b	A	T	12: 5,040,949 (GRCm39)	H206L	probably damaging	Het
Bmp2k	A	G	5: 97,235,937 (GRCm39)	Q1120R	probably benign	Het
Cdk18	G	A	1: 132,050,088 (GRCm39)	T29I	probably damaging	Het
Chrna3	T	A	9: 54,923,185 (GRCm39)	I208F	probably damaging	Het
Dhrs1	G	A	14: 55,978,729 (GRCm39)	P140S	possibly damaging	Het
Dnah14	C	T	1: 181,566,552 (GRCm39)	R2775C	probably damaging	Het
Fnip1	T	G	11: 54,393,437 (GRCm39)	N600K	probably benign	Het
Garin5b	T	C	7: 4,761,464 (GRCm39)	D416G	probably benign	Het
Kbtbd4	T	A	2: 90,739,635 (GRCm39)	V340E	probably damaging	Het
Kif26b	T	C	1: 178,755,871 (GRCm39)	V1995A	probably damaging	Het
Krt10	T	C	11: 99,278,221 (GRCm39)		probably null	Het
Macf1	T	C	4: 123,326,074 (GRCm39)	D3022G	probably benign	Het
Map3k13	C	T	16: 21,740,527 (GRCm39)	T618I	probably benign	Het
Mat1a	G	A	14: 40,843,379 (GRCm39)	V302M	probably damaging	Het
Med13l	T	C	5: 118,859,539 (GRCm39)	F242S	probably damaging	Het
Npffr2	A	T	5: 89,730,871 (GRCm39)	K267M	probably damaging	Het
Nup58	A	T	14: 60,460,672 (GRCm39)		probably null	Het
Papss2	A	G	19: 32,640,548 (GRCm39)	Y440C	possibly damaging	Het
Ppil4	T	A	10: 7,674,186 (GRCm39)	I110N	probably damaging	Het
Qrfpr	G	A	3: 36,234,414 (GRCm39)	T309I	probably damaging	Het
Rbl2	C	A	8: 91,796,998 (GRCm39)	S65R	probably benign	Het
Rchy1	G	A	5: 92,105,817 (GRCm39)	H44Y	probably damaging	Het
Slc19a3	T	C	1: 83,004,081 (GRCm39)	T7A	probably benign	Het
St7	C	T	6: 17,852,313 (GRCm39)	A233V	probably damaging	Het
Syn2	T	A	6: 115,258,059 (GRCm39)	S546T	probably benign	Het
Syne1	A	T	10: 5,168,645 (GRCm39)	Y5245*	probably null	Het
Trmt6	A	G	2: 132,654,073 (GRCm39)	W52R	probably benign	Het
Ubr4	G	A	4: 139,141,705 (GRCm39)	V1264M	probably damaging	Het
Ulk4	A	T	9: 120,970,960 (GRCm39)	V1004D	probably damaging	Het
Vmn2r111	T	C	17: 22,778,032 (GRCm39)	N549S	possibly damaging	Het
Vmn2r27	T	A	6: 124,169,369 (GRCm39)	H587L	possibly damaging	Het
Vmn2r79	A	G	7: 86,652,741 (GRCm39)	R478G	probably benign	Het
Zp2	T	C	7: 119,731,748 (GRCm39)	E669G	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
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
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'- TTCTGCTAACAGGCTTGCGG -3'
(R):5'- AAAGAGTTCGTGGAGCGCTAC -3'

Sequencing Primer
(F):5'- TGGAACTCATTCTGTAGCCCAGG -3'
(R):5'- CGCTACGAGAGGCCTTACAAG -3'

Posted On

2018-06-06