Mutagenetix > Incidental Mutation

Incidental Mutation 'R5782:Khdc4'

447779

Institutional Source

Beutler Lab

Gene Symbol

Khdc4

Ensembl Gene

ENSMUSG00000028060

Gene Name

KH domain containing 4, pre-mRNA splicing factor

Synonyms

2810403A07Rik

MMRRC Submission

043379-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.247) question?

Stock #

R5782 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

88593110-88620231 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 88618985 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glycine at position 563 (V563G)

Ref Sequence

ENSEMBL: ENSMUSP00000029696 (fasta)

Gene Model

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

AlphaFold

Q3TCX3

Predicted Effect

probably damaging
Transcript: ENSMUST00000029696
AA Change: V563G

PolyPhen 2 Score 0.958 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000029696
Gene: ENSMUSG00000028060
AA Change: V563G

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

noncoding transcript
Transcript: ENSMUST00000122484

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000197300

Predicted Effect

probably benign
Transcript: ENSMUST00000198042

SMART Domains

Protein: ENSMUSP00000142773
Gene: ENSMUSG00000028060

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 benign
Transcript: ENSMUST00000198078

SMART Domains

Protein: ENSMUSP00000142760
Gene: ENSMUSG00000028060

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: ENSMUST00000198721

Predicted Effect

probably benign
Transcript: ENSMUST00000199684

SMART Domains

Protein: ENSMUSP00000142353
Gene: ENSMUSG00000028060

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: ENSMUST00000200622

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.5%
20x: 95.8%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Actl9	A	T	17: 33,652,735 (GRCm39)	Q265L	probably benign	Het
Adamtsl3	T	A	7: 82,189,494 (GRCm39)		probably null	Het
Agt	A	T	8: 125,283,870 (GRCm39)		probably null	Het
Ankrd11	A	G	8: 123,626,756 (GRCm39)	L142P	probably damaging	Het
Arhgef19	C	A	4: 140,983,623 (GRCm39)	Q719K	probably damaging	Het
Armh3	A	G	19: 45,874,466 (GRCm39)	V569A	probably benign	Het
Atrnl1	G	T	19: 57,741,718 (GRCm39)	W1159L	possibly damaging	Het
Atxn2	T	C	5: 121,935,373 (GRCm39)	Y325H	probably damaging	Het
Brwd1	A	T	16: 95,844,243 (GRCm39)	Y770*	probably null	Het
Cdc20	T	C	4: 118,290,239 (GRCm39)	E474G	probably benign	Het
Cdk5rap3	A	G	11: 96,802,412 (GRCm39)	L254P	probably benign	Het
Cep83	A	T	10: 94,584,894 (GRCm39)	N333I	probably damaging	Het
Cox4i2	A	C	2: 152,606,731 (GRCm39)	D150A	probably damaging	Het
Cse1l	A	G	2: 166,770,921 (GRCm39)	I314M	probably damaging	Het
Cuedc1	A	G	11: 88,060,858 (GRCm39)	Y67C	probably damaging	Het
Cyp2j9	C	T	4: 96,462,142 (GRCm39)	V380I	probably benign	Het
Fancd2	A	G	6: 113,525,833 (GRCm39)	N302S	probably benign	Het
Foxa1	T	A	12: 57,589,302 (GRCm39)	H306L	probably benign	Het
Gse1	T	C	8: 121,293,260 (GRCm39)	S204P	probably damaging	Het
Hspa13	C	A	16: 75,554,985 (GRCm39)	R367L	probably damaging	Het
Kcnk2	T	G	1: 188,988,776 (GRCm39)	D267A	probably damaging	Het
Kctd18	A	G	1: 57,998,396 (GRCm39)	Y68H	probably damaging	Het
Klf7	C	T	1: 64,081,570 (GRCm39)	E253K	possibly damaging	Het
Lcn12	A	T	2: 25,383,769 (GRCm39)	F34I	probably damaging	Het
Lrrk2	A	T	15: 91,586,386 (GRCm39)	R401W	probably damaging	Het
Lzts1	A	T	8: 69,593,350 (GRCm39)	S86T	probably benign	Het
Mtres1	T	C	10: 43,408,899 (GRCm39)	I81M	probably benign	Het
Mtus1	T	A	8: 41,535,764 (GRCm39)	I651F	probably damaging	Het
Myl2	T	A	5: 122,242,933 (GRCm39)	F106L	probably damaging	Het
Neb	T	A	2: 52,154,059 (GRCm39)	K2351*	probably null	Het
Or14c45	T	A	7: 86,176,421 (GRCm39)	I152N	probably damaging	Het
Or52e5	T	C	7: 104,718,956 (GRCm39)	I94T	probably damaging	Het
Otogl	G	A	10: 107,612,978 (GRCm39)		silent	Het
Parg	A	T	14: 31,996,862 (GRCm39)	R318*	probably null	Het
Pcdhga3	C	T	18: 37,809,353 (GRCm39)	S602F	possibly damaging	Het
Pcnx2	A	G	8: 126,480,223 (GRCm39)	V2028A	probably damaging	Het
Pkhd1	T	C	1: 20,128,824 (GRCm39)	T3960A	probably benign	Het
Psen1	T	A	12: 83,759,233 (GRCm39)	H81Q	possibly damaging	Het
Psma6	A	G	12: 55,457,041 (GRCm39)	N109S	possibly damaging	Het
Ptpro	A	T	6: 137,376,496 (GRCm39)	I659F	possibly damaging	Het
Rap1gds1	C	G	3: 138,664,840 (GRCm39)	E288D	possibly damaging	Het
Reln	C	T	5: 22,223,054 (GRCm39)	R993K	probably benign	Het
Saxo1	T	A	4: 86,364,044 (GRCm39)	L146F	probably damaging	Het
Six4	A	G	12: 73,150,832 (GRCm39)	V571A	probably benign	Het
Slc2a10	C	A	2: 165,356,758 (GRCm39)	Y139*	probably null	Het
Slc34a1	A	G	13: 55,550,501 (GRCm39)	I66V	possibly damaging	Het
Slfn8	G	T	11: 82,907,867 (GRCm39)	N46K	probably damaging	Het
Smc6	G	C	12: 11,340,835 (GRCm39)	A496P	probably damaging	Het
Stk31	T	G	6: 49,446,070 (GRCm39)	N902K	probably benign	Het
Stk36	T	A	1: 74,644,584 (GRCm39)	Y114N	possibly damaging	Het
Sult2b1	C	T	7: 45,380,770 (GRCm39)	V271M	probably damaging	Het
Tenm4	A	G	7: 96,542,246 (GRCm39)	I1920V	probably benign	Het
Trbc2	A	G	6: 41,523,871 (GRCm39)		probably benign	Het
Trpc2	A	G	7: 101,733,186 (GRCm39)	D419G	possibly damaging	Het
Trpm7	T	C	2: 126,639,634 (GRCm39)	N1654S	probably benign	Het
Tsku	A	T	7: 98,002,057 (GRCm39)	D91E	probably damaging	Het
Ttn	T	A	2: 76,606,355 (GRCm39)	R18151S	probably damaging	Het
Tyr	C	T	7: 87,142,224 (GRCm39)	C112Y	probably damaging	Het
Ubash3a	G	A	17: 31,454,477 (GRCm39)	G435S	probably benign	Het
Vav1	T	C	17: 57,603,001 (GRCm39)	I51T	probably damaging	Het
Vmn2r61	T	A	7: 41,949,253 (GRCm39)	C558S	probably damaging	Het
Zan	C	T	5: 137,418,269 (GRCm39)	C2943Y	unknown	Het
Zfp1002	T	C	2: 150,097,438 (GRCm39)	E25G	probably benign	Het
Zfp267	T	C	3: 36,219,128 (GRCm39)	S384P	possibly damaging	Het
Zfp318	TGAAGAAGAAGAAGAAGAAGAAGAAGAAG	TGAAGAAGAAGAAGAAGAAGAAG	17: 46,723,440 (GRCm39)		probably benign	Het
Zfp575	C	A	7: 24,285,027 (GRCm39)	G205C	possibly damaging	Het
Zfp740	G	T	15: 102,116,801 (GRCm39)		probably benign	Het
Zzz3	A	G	3: 152,133,737 (GRCm39)	E265G	possibly 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
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
R6939:Khdc4	UTSW	3	88,593,824 (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'- GGCTACAAAATGGTGTCCAAC -3'
(R):5'- GAACAGGTCCCAGAGTCTTG -3'

Sequencing Primer
(F):5'- GGCTACAAAATGGTGTCCAACTAACC -3'
(R):5'- TCACTGAGGGTCAAAGCTCTGTC -3'

Posted On

2016-12-15