Mutagenetix > Incidental Mutation

Incidental Mutation 'R7904:Smyd4'

610176

Institutional Source

Beutler Lab

Gene Symbol

Smyd4

Ensembl Gene

ENSMUSG00000018809

Gene Name

SET and MYND domain containing 4

Synonyms

G430029E23Rik

MMRRC Submission

045956-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7904 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

75239259-75296531 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 75240613 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 36 (I36T)

Ref Sequence

ENSEMBL: ENSMUSP00000047505 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000000767] [ENSMUST00000044530] [ENSMUST00000092907]

AlphaFold

Q8BTK5

Predicted Effect

probably benign
Transcript: ENSMUST00000000767

SMART Domains

Protein: ENSMUSP00000000767
Gene: ENSMUSG00000000751

Domain	Start	End	E-Value	Type
Pfam:Rep-A_N	5	93	7.2e-30	PFAM
low complexity region	145	175	N/A	INTRINSIC
Pfam:tRNA_anti-codon	227	316	5e-13	PFAM
Pfam:REPA_OB_2	335	432	5e-37	PFAM
Pfam:Rep_fac-A_C	491	636	4.5e-57	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000044530
AA Change: I36T

PolyPhen 2 Score 0.795 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000047505
Gene: ENSMUSG00000018809
AA Change: I36T

Domain	Start	End	E-Value	Type
Pfam:TPR_11	65	132	2.4e-10	PFAM
SET	231	576	4.85e-1	SMART
Blast:TPR	694	726	1e-6	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000092907

SMART Domains

Protein: ENSMUSP00000090585
Gene: ENSMUSG00000000751

Domain	Start	End	E-Value	Type
Pfam:Rep-A_N	5	104	4.3e-35	PFAM
low complexity region	124	154	N/A	INTRINSIC
Pfam:tRNA_anti-codon	206	295	8.4e-13	PFAM
SCOP:d1fgua2	308	435	8e-46	SMART
Pfam:Rep_fac-A_C	470	615	9.2e-56	PFAM

Meta Mutation Damage Score

0.1478

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

Validation Efficiency

97% (72/74)

MGI Phenotype

PHENOTYPE: Mice homozygous for a knock-out allele exhibit testicular degeneration and atrophy. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam8	G	A	7: 139,567,591 (GRCm39)	T384I	probably benign	Het
Astn1	T	C	1: 158,424,886 (GRCm39)	F691L	probably benign	Het
Azgp1	A	G	5: 137,985,869 (GRCm39)	E164G	probably damaging	Het
Bdp1	A	G	13: 100,177,944 (GRCm39)	V1975A	probably benign	Het
Cactin	T	C	10: 81,161,699 (GRCm39)	Y744H	possibly damaging	Het
Clstn1	T	A	4: 149,698,594 (GRCm39)	I60N	probably benign	Het
Col16a1	T	A	4: 129,948,001 (GRCm39)	C240*	probably null	Het
Col6a5	T	C	9: 105,805,720 (GRCm39)	D1062G	unknown	Het
Csmd2	T	C	4: 128,313,346 (GRCm39)	L1341P		Het
Cyp51	A	T	5: 4,150,173 (GRCm39)	F183L	probably damaging	Het
Dbnl	T	A	11: 5,741,779 (GRCm39)		probably null	Het
Ddx60	G	A	8: 62,430,924 (GRCm39)	V820I	possibly damaging	Het
Dnaaf9	A	T	2: 130,633,923 (GRCm39)		probably null	Het
Dnah11	T	A	12: 117,867,003 (GRCm39)	D4046V	possibly damaging	Het
Dnah6	G	A	6: 73,112,450 (GRCm39)		probably null	Het
Dnttip1	A	G	2: 164,589,472 (GRCm39)	Y89C	probably benign	Het
Efr3a	T	A	15: 65,696,527 (GRCm39)	V144E	probably damaging	Het
Epha8	T	C	4: 136,659,050 (GRCm39)	Q868R	possibly damaging	Het
Ercc5	G	T	1: 44,214,998 (GRCm39)		probably null	Het
Fam118a	A	G	15: 84,929,834 (GRCm39)	S21G	probably damaging	Het
Fam171b	T	C	2: 83,683,849 (GRCm39)	I122T	probably damaging	Het
Fat4	T	A	3: 38,941,690 (GRCm39)	S194R	probably damaging	Het
Fcho2	T	A	13: 98,932,871 (GRCm39)	T44S	possibly damaging	Het
Gm21698	C	A	5: 26,189,256 (GRCm39)	L232F	probably benign	Het
Gpr149	T	A	3: 62,502,356 (GRCm39)	D500V	probably benign	Het
Gpx8	T	A	13: 113,182,035 (GRCm39)	T133S	probably benign	Het
Hdlbp	A	T	1: 93,351,092 (GRCm39)	I542N	probably damaging	Het
Hid1	G	A	11: 115,246,187 (GRCm39)	S361F	probably damaging	Het
Igdcc4	C	A	9: 65,041,801 (GRCm39)	A1076E	probably benign	Het
Il4ra	A	G	7: 125,164,845 (GRCm39)	K7E	probably benign	Het
Inka2	T	C	3: 105,623,730 (GRCm39)	C35R	probably damaging	Het
Itga9	G	T	9: 118,706,294 (GRCm39)		probably null	Het
Kif5c	T	C	2: 49,591,095 (GRCm39)	S316P	probably damaging	Het
Kmt5c	A	T	7: 4,749,158 (GRCm39)	T264S	probably damaging	Het
Litafd	A	G	16: 8,501,681 (GRCm39)	H61R		Het
Lrrc18	A	G	14: 32,731,052 (GRCm39)	N197S	probably benign	Het
Mcoln1	C	A	8: 3,558,356 (GRCm39)	D203E	probably benign	Het
Mitf	T	C	6: 97,990,671 (GRCm39)	V358A	probably damaging	Het
Mki67	A	T	7: 135,294,816 (GRCm39)	L3161Q	possibly damaging	Het
Mmp20	T	A	9: 7,644,076 (GRCm39)	F255I	possibly damaging	Het
Muc16	T	C	9: 18,566,946 (GRCm39)	T1858A	unknown	Het
Mug1	G	A	6: 121,828,424 (GRCm39)	V279I	probably benign	Het
Or6c68	T	C	10: 129,157,665 (GRCm39)	Y58H	probably damaging	Het
Otulin	G	T	15: 27,630,580 (GRCm39)	A39E	probably benign	Het
Pcdh17	A	T	14: 84,685,924 (GRCm39)	D797V	possibly damaging	Het
Pdlim5	G	A	3: 142,018,154 (GRCm39)	S147L	probably damaging	Het
Peg10	GC	GCTCC	6: 4,756,452 (GRCm39)		probably benign	Het
Ppp2r1a	T	G	17: 21,182,003 (GRCm39)		probably null	Het
Ranbp6	T	C	19: 29,789,813 (GRCm39)	I180V	probably benign	Het
Rbm27	G	T	18: 42,465,921 (GRCm39)	R869L	probably damaging	Het
Rtn4r	A	G	16: 17,969,349 (GRCm39)	D259G	probably benign	Het
Ryr3	T	C	2: 112,611,369 (GRCm39)	E2271G	probably damaging	Het
Sbk1	A	G	7: 125,891,208 (GRCm39)	Y214C	probably damaging	Het
Scg3	C	T	9: 75,551,149 (GRCm39)	E459K	probably damaging	Het
Scin	T	G	12: 40,126,999 (GRCm39)	E449D	probably damaging	Het
Sel1l3	T	C	5: 53,297,166 (GRCm39)	K760R	probably benign	Het
Sh3pxd2a	A	G	19: 47,308,753 (GRCm39)	L145S	possibly damaging	Het
Sh3yl1	A	G	12: 30,991,995 (GRCm39)	D188G	probably benign	Het
Slc38a1	A	T	15: 96,521,921 (GRCm39)	L13Q	possibly damaging	Het
Spata31f1a	A	G	4: 42,850,765 (GRCm39)	S464P	possibly damaging	Het
Stab2	A	T	10: 86,790,056 (GRCm39)	L570*	probably null	Het
Tg	G	T	15: 66,577,128 (GRCm39)	A1484S	probably benign	Het
Tm7sf2	A	T	19: 6,118,942 (GRCm39)	N677K	probably damaging	Het
Tmem235	T	G	11: 117,751,717 (GRCm39)	L47R	probably damaging	Het
Tmem87a	A	G	2: 120,210,198 (GRCm39)	S252P	probably damaging	Het
Unc13b	A	G	4: 43,217,075 (GRCm39)	D458G	probably benign	Het
Wfdc1	A	G	8: 120,406,770 (GRCm39)		probably null	Het
Wnt16	A	G	6: 22,297,989 (GRCm39)	Y285C	probably damaging	Het
Wwc2	A	T	8: 48,309,270 (GRCm39)	N837K	unknown	Het
Xdh	A	G	17: 74,229,467 (GRCm39)	F329L	probably benign	Het
Yaf2	G	T	15: 93,183,466 (GRCm39)	H115N	probably benign	Het
Zbtb16	G	T	9: 48,744,272 (GRCm39)	N13K	probably damaging	Het
Zfhx3	A	T	8: 109,677,695 (GRCm39)	D2915V	probably damaging	Het
Zfp236	A	T	18: 82,627,507 (GRCm39)	V1564E	possibly damaging	Het
Zfp407	G	T	18: 84,579,381 (GRCm39)	H577Q	not run	Het

Other mutations in Smyd4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00777:Smyd4	APN	11	75,281,634 (GRCm39)	missense	probably benign
IGL02372:Smyd4	APN	11	75,281,111 (GRCm39)	nonsense	probably null
IGL02390:Smyd4	APN	11	75,278,332 (GRCm39)	splice site	probably null
IGL02492:Smyd4	APN	11	75,294,252 (GRCm39)	missense	probably benign
IGL02504:Smyd4	APN	11	75,281,507 (GRCm39)	missense	probably damaging	1.00
IGL02623:Smyd4	APN	11	75,280,890 (GRCm39)	splice site	probably benign
IGL02661:Smyd4	APN	11	75,281,767 (GRCm39)	nonsense	probably null
IGL03084:Smyd4	APN	11	75,281,433 (GRCm39)	missense	probably benign	0.00
PIT4431001:Smyd4	UTSW	11	75,294,339 (GRCm39)	missense	probably damaging	1.00
R0507:Smyd4	UTSW	11	75,290,534 (GRCm39)	missense	possibly damaging	0.69
R0834:Smyd4	UTSW	11	75,281,958 (GRCm39)	missense	possibly damaging	0.94
R1075:Smyd4	UTSW	11	75,291,164 (GRCm39)	missense	probably damaging	1.00
R1215:Smyd4	UTSW	11	75,281,121 (GRCm39)	missense	possibly damaging	0.96
R1759:Smyd4	UTSW	11	75,273,192 (GRCm39)	missense	probably damaging	1.00
R2496:Smyd4	UTSW	11	75,281,927 (GRCm39)	missense	probably benign	0.03
R2862:Smyd4	UTSW	11	75,280,962 (GRCm39)	missense	probably benign	0.12
R4033:Smyd4	UTSW	11	75,240,580 (GRCm39)	missense	probably benign	0.06
R4655:Smyd4	UTSW	11	75,281,558 (GRCm39)	missense	probably damaging	1.00
R4775:Smyd4	UTSW	11	75,282,018 (GRCm39)	missense	probably damaging	1.00
R4801:Smyd4	UTSW	11	75,294,010 (GRCm39)	missense	probably damaging	1.00
R4802:Smyd4	UTSW	11	75,294,010 (GRCm39)	missense	probably damaging	1.00
R4963:Smyd4	UTSW	11	75,273,120 (GRCm39)	missense	probably benign	0.01
R5306:Smyd4	UTSW	11	75,292,984 (GRCm39)	missense	probably benign	0.00
R5327:Smyd4	UTSW	11	75,281,765 (GRCm39)	missense	probably damaging	1.00
R5386:Smyd4	UTSW	11	75,280,982 (GRCm39)	missense	probably damaging	1.00
R5578:Smyd4	UTSW	11	75,295,602 (GRCm39)	missense	probably benign	0.03
R7038:Smyd4	UTSW	11	75,281,340 (GRCm39)	missense	probably damaging	1.00
R7271:Smyd4	UTSW	11	75,281,325 (GRCm39)	missense	possibly damaging	0.90
R7312:Smyd4	UTSW	11	75,281,082 (GRCm39)	missense	probably benign	0.18
R7576:Smyd4	UTSW	11	75,281,032 (GRCm39)	missense	probably benign	0.03
R8387:Smyd4	UTSW	11	75,292,984 (GRCm39)	missense	probably benign	0.00
R8816:Smyd4	UTSW	11	75,281,232 (GRCm39)	missense	probably benign	0.24
R9235:Smyd4	UTSW	11	75,295,689 (GRCm39)	missense	probably benign	0.00
R9436:Smyd4	UTSW	11	75,293,017 (GRCm39)	missense	probably damaging	1.00
R9786:Smyd4	UTSW	11	75,281,625 (GRCm39)	missense	probably benign	0.06
Z1176:Smyd4	UTSW	11	75,290,440 (GRCm39)	missense	probably benign	0.03

Predicted Primers

PCR Primer
(F):5'- CGTGTCACTTGGTAGGATGAAATC -3'
(R):5'- CTGGGACGACAGCAAGATAC -3'

Sequencing Primer
(F):5'- CTTGGTAGGATGAAATCTCGATTTTC -3'
(R):5'- CCATTCTATAATCACAGACTAGGGAG -3'

Posted On

2019-12-20