Mutagenetix > Incidental Mutation

Incidental Mutation 'R9790:Jmjd6'

735903

Institutional Source

Beutler Lab

Gene Symbol

Jmjd6

Ensembl Gene

ENSMUSG00000056962

Gene Name

jumonji domain containing 6

Synonyms

5730436I23Rik, Ptdsr, PSR, PtdSerR

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9790 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

116728258-116734275 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 116733438 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 80 (S80P)

Ref Sequence

ENSEMBL: ENSMUSP00000047570 (fasta)

Gene Model

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

AlphaFold

Q9ERI5

Predicted Effect

probably benign
Transcript: ENSMUST00000047616
AA Change: S80P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000047570
Gene: ENSMUSG00000056962
AA Change: S80P

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

probably benign
Transcript: ENSMUST00000132593

Predicted Effect

probably benign
Transcript: ENSMUST00000140349
AA Change: S32P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000120850
Gene: ENSMUSG00000056962
AA Change: S32P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000140513
AA Change: S37P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000115086
Gene: ENSMUSG00000056962
AA Change: S37P

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

Predicted Effect

probably benign
Transcript: ENSMUST00000140869

Predicted Effect

probably benign
Transcript: ENSMUST00000142495
AA Change: S80P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000117922
Gene: ENSMUSG00000056962
AA Change: S80P

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

Coding Region Coverage

1x: 99.9%
3x: 99.8%
10x: 99.3%
20x: 98.4%

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: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb1a	T	C	5: 8,748,604 (GRCm39)	Y312H	probably damaging	Het
Abcc10	A	T	17: 46,633,185 (GRCm39)	I549N	probably damaging	Het
Agpat2	A	G	2: 26,486,395 (GRCm39)	Y134H	probably damaging	Het
Alms1	A	G	6: 85,596,425 (GRCm39)	D417G	probably benign	Het
Apol11b	T	A	15: 77,519,475 (GRCm39)	I202F	probably benign	Het
Arap1	C	A	7: 101,037,376 (GRCm39)	Q468K	probably benign	Het
Arhgef4	T	C	1: 34,832,445 (GRCm39)		probably null	Het
Asap3	A	T	4: 135,961,914 (GRCm39)	N285I	probably damaging	Het
Aspm	A	T	1: 139,408,375 (GRCm39)	I2421F	probably damaging	Het
Banp	C	A	8: 122,701,285 (GRCm39)	D17E	probably benign	Het
Bsx	T	G	9: 40,788,905 (GRCm39)	V154G	probably damaging	Het
Cacnb1	T	C	11: 97,900,186 (GRCm39)	D324G	probably damaging	Het
Ccdc170	A	T	10: 4,483,957 (GRCm39)		probably null	Het
Ccdc187	T	C	2: 26,171,227 (GRCm39)	H417R	probably benign	Het
Cct4	T	A	11: 22,949,070 (GRCm39)	M272K	probably damaging	Het
Chd9	A	G	8: 91,760,417 (GRCm39)	E2054G	possibly damaging	Het
Ctnnal1	A	T	4: 56,844,584 (GRCm39)	S127T	possibly damaging	Het
Cttnbp2	T	A	6: 18,376,027 (GRCm39)	H1504L	probably benign	Het
Cyp4a29	T	A	4: 115,108,380 (GRCm39)	M368K	probably damaging	Het
Dhx32	A	G	7: 133,326,267 (GRCm39)	F527L	probably benign	Het
Foxk1	T	C	5: 142,387,739 (GRCm39)	V154A	probably damaging	Het
Frem3	G	A	8: 81,339,890 (GRCm39)	E728K	probably benign	Het
Garem2	C	A	5: 30,319,747 (GRCm39)	A403E	probably benign	Het
Gemin5	G	A	11: 58,020,846 (GRCm39)	Q1114*	probably null	Het
Gm11567	C	T	11: 99,770,274 (GRCm39)	R71C	unknown	Het
Gm13272	T	C	4: 88,698,442 (GRCm39)	V119A	probably benign	Het
Gpc6	T	A	14: 117,163,435 (GRCm39)	C30S	probably damaging	Het
Gprc6a	A	C	10: 51,491,395 (GRCm39)	F785V	probably damaging	Het
Hormad1	T	C	3: 95,494,693 (GRCm39)	V368A	probably benign	Het
Hsd17b4	G	A	18: 50,324,907 (GRCm39)		probably null	Het
Idh2	TCCCAGG	T	7: 79,748,079 (GRCm39)		probably benign	Het
Il17ra	C	T	6: 120,459,240 (GRCm39)	S797F	probably damaging	Het
Klhdc2	T	A	12: 69,346,995 (GRCm39)	N53K	probably benign	Het
Klhl30	C	T	1: 91,282,089 (GRCm39)	P230L	probably benign	Het
Marchf1	C	A	8: 66,729,339 (GRCm39)	A46E	probably benign	Het
Mast4	T	C	13: 102,890,705 (GRCm39)	T1050A	probably benign	Het
Mpp7	T	C	18: 7,355,049 (GRCm39)	N459S	probably benign	Het
Mtfr1l	A	G	4: 134,258,063 (GRCm39)	V53A	probably benign	Het
Myh11	T	A	16: 14,025,992 (GRCm39)	E1326V		Het
Myh3	A	G	11: 66,992,005 (GRCm39)	E1850G	probably damaging	Het
Myo16	A	G	8: 10,619,925 (GRCm39)	D1492G	unknown	Het
Myo3b	C	A	2: 70,180,287 (GRCm39)	H1219Q	probably benign	Het
Nphp4	A	T	4: 152,646,605 (GRCm39)	Q1379L	probably null	Het
Or8g30	C	T	9: 39,230,815 (GRCm39)	V32I	probably benign	Het
Or9q1	A	G	19: 13,804,914 (GRCm39)	I282T	probably benign	Het
Osbpl6	T	G	2: 76,385,361 (GRCm39)	L265R	probably damaging	Het
Pld4	A	G	12: 112,734,862 (GRCm39)	T440A	probably damaging	Het
Prr14	T	C	7: 127,071,128 (GRCm39)	M1T	probably null	Het
Ptger4	A	T	15: 5,273,178 (GRCm39)	M1K	probably null	Het
Ptpn22	A	T	3: 103,795,842 (GRCm39)	T608S	possibly damaging	Het
S1pr2	A	G	9: 20,879,319 (GRCm39)	W170R	probably damaging	Het
Specc1l	A	G	10: 75,066,603 (GRCm39)	I17M	probably benign	Het
Spmap1	T	A	11: 97,666,594 (GRCm39)	I31F	probably benign	Het
Sptbn4	C	G	7: 27,071,662 (GRCm39)	G1601R	probably damaging	Het
Sqor	C	T	2: 122,626,912 (GRCm39)	P11L	probably benign	Het
Stac2	T	C	11: 97,934,449 (GRCm39)	D85G	probably benign	Het
Svs5	G	A	2: 164,078,918 (GRCm39)	Q330*	probably null	Het
Taar7e	A	G	10: 23,913,554 (GRCm39)	I15V	probably benign	Het
Tcf4	A	T	18: 69,770,007 (GRCm39)	Y275F	probably damaging	Het
Tenm4	A	G	7: 96,538,046 (GRCm39)	N1873S	probably damaging	Het
Tert	T	A	13: 73,775,648 (GRCm39)	V133D	probably benign	Het
Tfap2a	T	A	13: 40,870,658 (GRCm39)	N410I	probably damaging	Het
Tjp3	A	T	10: 81,109,694 (GRCm39)	D836E	probably benign	Het
Tox3	A	T	8: 90,975,206 (GRCm39)	M475K	unknown	Het
Traf4	A	T	11: 78,050,979 (GRCm39)	D392E	probably damaging	Het
Vav2	A	G	2: 27,181,825 (GRCm39)	L338P	probably damaging	Het
Vmn1r81	T	C	7: 11,994,113 (GRCm39)	N165S	probably benign	Het
Vmn2r9	A	T	5: 108,995,409 (GRCm39)	V413E	probably damaging	Het
Wdr7	A	T	18: 63,911,059 (GRCm39)	D817V	probably damaging	Het
Zbtb38	G	A	9: 96,570,700 (GRCm39)	S128L	probably damaging	Het
Zfhx4	T	A	3: 5,464,922 (GRCm39)	H1718Q	probably damaging	Het
Zfp945	G	A	17: 23,071,228 (GRCm39)	H245Y	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
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
R9791:Jmjd6	UTSW	11	116,733,438 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- CCCGCGTATTGGAAAAGATCATC -3'
(R):5'- ATCCGCCACTGGACTTGTTC -3'

Sequencing Primer
(F):5'- GGCACCTTGTAGTCTTCCAAAAG -3'
(R):5'- GGACTTGTTCCAGTGTCCTAACG -3'

Posted On

2022-11-14