Mutagenetix > Incidental Mutation

Incidental Mutation 'R6939:Khdc4'

540414

Institutional Source

Beutler Lab

Gene Symbol

Khdc4

Ensembl Gene

ENSMUSG00000028060

Gene Name

KH domain containing 4, pre-mRNA splicing factor

Synonyms

2810403A07Rik

MMRRC Submission

045053-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.297) question?

Stock #

R6939 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

88593110-88620231 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 88593824 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 71 (M71K)

Ref Sequence

ENSEMBL: ENSMUSP00000142760 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029696] [ENSMUST00000198042] [ENSMUST00000198078] [ENSMUST00000199684]

AlphaFold

Q3TCX3

Predicted Effect

possibly damaging
Transcript: ENSMUST00000029696
AA Change: M71K

PolyPhen 2 Score 0.794 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000029696
Gene: ENSMUSG00000028060
AA Change: M71K

Domain	Start	End	E-Value	Type
low complexity region	21	66	N/A	INTRINSIC
Blast:KH	103	185	2e-28	BLAST
PDB:2YQR\|A	229	340	6e-76	PDB
Blast:KH	233	319	1e-36	BLAST
SCOP:d1k1ga_	233	327	4e-16	SMART
low complexity region	344	384	N/A	INTRINSIC
low complexity region	425	436	N/A	INTRINSIC
low complexity region	442	458	N/A	INTRINSIC
low complexity region	499	510	N/A	INTRINSIC
low complexity region	566	579	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000198042
AA Change: M71K

PolyPhen 2 Score 0.614 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000142773
Gene: ENSMUSG00000028060
AA Change: M71K

Domain	Start	End	E-Value	Type
low complexity region	21	66	N/A	INTRINSIC
Blast:KH	103	185	7e-29	BLAST
PDB:2YQR\|A	229	340	2e-77	PDB
Blast:KH	233	319	2e-37	BLAST
SCOP:d1k1ga_	233	327	3e-16	SMART
low complexity region	344	384	N/A	INTRINSIC
low complexity region	425	436	N/A	INTRINSIC
low complexity region	442	458	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000198078
AA Change: M71K

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000142760
Gene: ENSMUSG00000028060
AA Change: M71K

Domain	Start	End	E-Value	Type
low complexity region	21	66	N/A	INTRINSIC
Blast:KH	103	185	5e-29	BLAST
PDB:2YQR\|A	229	340	1e-77	PDB
Blast:KH	233	319	3e-37	BLAST
SCOP:d1k1ga_	233	327	4e-17	SMART
low complexity region	410	421	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000198351

Predicted Effect

possibly damaging
Transcript: ENSMUST00000199684
AA Change: M71K

PolyPhen 2 Score 0.614 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000142353
Gene: ENSMUSG00000028060
AA Change: M71K

Domain	Start	End	E-Value	Type
low complexity region	21	66	N/A	INTRINSIC
Blast:KH	103	185	7e-29	BLAST
PDB:2YQR\|A	229	340	2e-77	PDB
Blast:KH	233	319	2e-37	BLAST
SCOP:d1k1ga_	233	327	3e-16	SMART
low complexity region	344	384	N/A	INTRINSIC
low complexity region	425	436	N/A	INTRINSIC
low complexity region	442	458	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000200364

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000200588

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.3%
20x: 97.9%

Validation Efficiency

99% (66/67)

Allele List at MGI

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A1bg	G	A	15: 60,792,244 (GRCm39)	P128L	probably damaging	Het
Acsm3	T	C	7: 119,377,678 (GRCm39)	V401A	probably damaging	Het
Arhgef11	C	A	3: 87,594,227 (GRCm39)	N93K	probably damaging	Het
C1ra	G	A	6: 124,489,760 (GRCm39)		probably null	Het
Camk2a	A	G	18: 61,091,226 (GRCm39)	E236G	probably damaging	Het
Cav2	C	A	6: 17,281,410 (GRCm39)	D17E	possibly damaging	Het
Ccdc149	T	C	5: 52,533,607 (GRCm39)	S520G	probably benign	Het
Chd4	C	A	6: 125,083,501 (GRCm39)	H674Q	probably damaging	Het
Clrn2	A	T	5: 45,611,096 (GRCm39)		probably benign	Het
Cntnap1	A	C	11: 101,077,337 (GRCm39)	I1000L	probably damaging	Het
Cyp2c67	T	C	19: 39,631,778 (GRCm39)	T140A	possibly damaging	Het
D7Ertd443e	T	C	7: 133,966,208 (GRCm39)		probably null	Het
Dcdc2c	G	T	12: 28,591,496 (GRCm39)	Q131K	probably benign	Het
Dmpk	T	A	7: 18,822,149 (GRCm39)	V369E	probably damaging	Het
Dnah11	A	T	12: 118,070,297 (GRCm39)	W1503R	probably damaging	Het
Dnai7	A	G	6: 145,120,945 (GRCm39)	F625L	possibly damaging	Het
Dok2	T	C	14: 71,013,045 (GRCm39)	V71A	probably benign	Het
Dqx1	A	T	6: 83,036,446 (GRCm39)	Q150L	probably damaging	Het
Extl3	A	G	14: 65,304,189 (GRCm39)	I740T	possibly damaging	Het
Fan1	T	A	7: 64,022,234 (GRCm39)	N340Y	probably damaging	Het
Fat2	C	T	11: 55,143,300 (GRCm39)	W4183*	probably null	Het
Fkrp	C	T	7: 16,545,751 (GRCm39)	R37Q	probably benign	Het
Frem3	A	G	8: 81,341,774 (GRCm39)	K1356E	probably benign	Het
Fus	A	T	7: 127,571,741 (GRCm39)		probably benign	Het
Gabarapl2	C	A	8: 112,669,201 (GRCm39)	S53*	probably null	Het
Gjd3	A	C	11: 102,691,733 (GRCm39)	M90R	probably damaging	Het
Gm30083	C	T	14: 33,725,557 (GRCm39)		probably null	Het
Gm7356	T	A	17: 14,221,387 (GRCm39)	Y214F	probably benign	Het
Hexd	A	T	11: 121,113,164 (GRCm39)	D533V	probably benign	Het
Ift172	G	A	5: 31,414,930 (GRCm39)	A1364V	probably damaging	Het
Ighmbp2	A	T	19: 3,326,907 (GRCm39)	F186Y	probably damaging	Het
Inpp5e	C	A	2: 26,297,774 (GRCm39)		probably null	Het
Iqcb1	A	G	16: 36,660,274 (GRCm39)	T146A	possibly damaging	Het
Kcnmb2	A	G	3: 32,252,465 (GRCm39)	Y222C	probably damaging	Het
Kdm6b	A	G	11: 69,297,588 (GRCm39)	W284R	probably damaging	Het
Ksr2	T	A	5: 117,903,626 (GRCm39)	*952R	probably null	Het
Ldlrap1	C	A	4: 134,495,285 (GRCm39)		probably benign	Het
Mpdu1	G	A	11: 69,548,881 (GRCm39)		probably benign	Het
Mrgprh	A	T	17: 13,095,822 (GRCm39)	T21S	probably benign	Het
Muc16	T	A	9: 18,549,833 (GRCm39)	T5487S	probably benign	Het
Mydgf	A	G	17: 56,490,737 (GRCm39)		probably null	Het
Napa	T	C	7: 15,849,182 (GRCm39)	C241R	possibly damaging	Het
Or10ab4	C	A	7: 107,654,312 (GRCm39)	A41E	possibly damaging	Het
Or10n7-ps1	T	C	9: 39,598,187 (GRCm39)	T18A	possibly damaging	Het
Or5k17	A	T	16: 58,746,648 (GRCm39)	Y95*	probably null	Het
Pla2g4f	A	T	2: 120,137,782 (GRCm39)	L326Q	probably damaging	Het
Pramel16	T	C	4: 143,675,366 (GRCm39)	T487A	probably benign	Het
Psme4	T	A	11: 30,787,291 (GRCm39)	Y1029N	probably damaging	Het
Ptprj	T	C	2: 90,289,858 (GRCm39)	T707A	possibly damaging	Het
Raet1e	T	A	10: 22,050,256 (GRCm39)	M13K	possibly damaging	Het
Rftn2	T	C	1: 55,233,508 (GRCm39)		probably null	Het
Rmi1	A	G	13: 58,557,169 (GRCm39)	I473V	probably benign	Het
Rps6ka4	A	G	19: 6,815,437 (GRCm39)	F186L	probably damaging	Het
Ryr1	T	A	7: 28,751,751 (GRCm39)	M3672L	possibly damaging	Het
Smarca5	A	T	8: 81,431,949 (GRCm39)	C890S	possibly damaging	Het
Spata31d1e	T	A	13: 59,889,872 (GRCm39)	K231N	possibly damaging	Het
Tdrd12	C	T	7: 35,185,024 (GRCm39)		probably null	Het
Tecta	T	C	9: 42,259,293 (GRCm39)	N1530S	probably damaging	Het
Tenm4	G	A	7: 96,202,703 (GRCm39)	R106H	probably benign	Het
Tmem94	A	G	11: 115,676,656 (GRCm39)	S54G	possibly damaging	Het
Tnk2	T	C	16: 32,482,696 (GRCm39)	V41A	probably damaging	Het
Trpm1	A	G	7: 63,918,045 (GRCm39)	T462A	probably benign	Het
Tsg101	T	C	7: 46,556,847 (GRCm39)	T61A	probably benign	Het
Usp42	T	C	5: 143,713,724 (GRCm39)	N17D	probably damaging	Het
Zfp607a	T	A	7: 27,578,473 (GRCm39)	C514*	probably null	Het
Zfp866	G	T	8: 70,218,871 (GRCm39)	Q250K	probably damaging	Het

Other mutations in Khdc4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R0085:Khdc4	UTSW	3	88,619,046 (GRCm39)	missense	probably damaging	0.99
R0271:Khdc4	UTSW	3	88,593,636 (GRCm39)	splice site	probably benign
R1160:Khdc4	UTSW	3	88,616,169 (GRCm39)	missense	probably damaging	0.99
R2348:Khdc4	UTSW	3	88,616,183 (GRCm39)	missense	probably benign	0.01
R3121:Khdc4	UTSW	3	88,596,599 (GRCm39)	missense	probably damaging	1.00
R3546:Khdc4	UTSW	3	88,600,443 (GRCm39)	splice site	probably benign
R3548:Khdc4	UTSW	3	88,600,443 (GRCm39)	splice site	probably benign
R4688:Khdc4	UTSW	3	88,593,824 (GRCm39)	missense	probably damaging	1.00
R5249:Khdc4	UTSW	3	88,604,032 (GRCm39)	missense	probably damaging	1.00
R5393:Khdc4	UTSW	3	88,603,913 (GRCm39)	missense	probably benign	0.08
R5558:Khdc4	UTSW	3	88,600,403 (GRCm39)	missense	probably damaging	0.98
R5579:Khdc4	UTSW	3	88,607,582 (GRCm39)	missense	probably benign
R5782:Khdc4	UTSW	3	88,618,985 (GRCm39)	missense	probably damaging	0.96
R5809:Khdc4	UTSW	3	88,616,192 (GRCm39)	missense	probably damaging	0.96
R6415:Khdc4	UTSW	3	88,607,279 (GRCm39)	missense	probably benign	0.25
R6566:Khdc4	UTSW	3	88,618,961 (GRCm39)	missense	probably damaging	0.99
R6765:Khdc4	UTSW	3	88,593,736 (GRCm39)	missense	probably damaging	1.00
R7248:Khdc4	UTSW	3	88,600,886 (GRCm39)	missense	probably damaging	1.00
R7311:Khdc4	UTSW	3	88,619,002 (GRCm39)	missense	probably damaging	0.96
R7852:Khdc4	UTSW	3	88,604,043 (GRCm39)	missense	probably benign	0.06
R8294:Khdc4	UTSW	3	88,603,915 (GRCm39)	missense	probably damaging	0.98
R8948:Khdc4	UTSW	3	88,617,219 (GRCm39)	missense	probably damaging	0.99
R8988:Khdc4	UTSW	3	88,607,286 (GRCm39)	missense	probably benign	0.00
R9053:Khdc4	UTSW	3	88,596,582 (GRCm39)	missense	probably damaging	1.00
R9221:Khdc4	UTSW	3	88,593,853 (GRCm39)	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- CTACACAAAGGAAGGCCGTG -3'
(R):5'- ATACTCCCAAACGTGATCTTCACTC -3'

Sequencing Primer
(F):5'- TGGGCCTCAGGATTTCCC -3'
(R):5'- AACGTGATCTTCACTCTAACCGG -3'

Posted On

2018-11-06