Mutagenetix > Incidental Mutation

Incidental Mutation 'R6765:Khdc4'

531850

Institutional Source

Beutler Lab

Gene Symbol

Khdc4

Ensembl Gene

ENSMUSG00000028060

Gene Name

KH domain containing 4, pre-mRNA splicing factor

Synonyms

2810403A07Rik

MMRRC Submission

044881-MU

Accession Numbers

Essential gene?

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

Stock #

R6765 (G1)

Quality Score

138.008

Status

Validated

Chromosome

Chromosomal Location

88593110-88620231 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 88593736 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Tryptophan at position 42 (G42W)

Ref Sequence

ENSEMBL: ENSMUSP00000142760 (fasta)

Gene Model

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

AlphaFold

Q3TCX3

Predicted Effect

probably damaging
Transcript: ENSMUST00000029696
AA Change: G42W

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000029696
Gene: ENSMUSG00000028060
AA Change: G42W

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

probably damaging
Transcript: ENSMUST00000198042
AA Change: G42W

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000142773
Gene: ENSMUSG00000028060
AA Change: G42W

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: G42W

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000142760
Gene: ENSMUSG00000028060
AA Change: G42W

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

probably damaging
Transcript: ENSMUST00000199684
AA Change: G42W

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000142353
Gene: ENSMUSG00000028060
AA Change: G42W

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

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.3%
20x: 95.5%

Validation Efficiency

100% (58/58)

Allele List at MGI

Other mutations in this stock

Total: 58 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamtsl3	C	A	7: 82,216,232 (GRCm39)	D878E	possibly damaging	Het
Adipor2	A	C	6: 119,334,203 (GRCm39)	F336V	possibly damaging	Het
Akt3	A	T	1: 176,877,756 (GRCm39)	Y337*	probably null	Het
Aoc1	A	G	6: 48,882,871 (GRCm39)	N249S	probably benign	Het
Ap1b1	T	A	11: 4,969,427 (GRCm39)	L261Q	probably damaging	Het
Ap3b1	T	A	13: 94,599,017 (GRCm39)	D530E	probably benign	Het
Arid4b	T	A	13: 14,361,900 (GRCm39)	M788K	possibly damaging	Het
Atp2c2	A	T	8: 120,479,756 (GRCm39)	I762F	probably damaging	Het
Bhlhe23	C	A	2: 180,418,136 (GRCm39)	R134L	probably damaging	Het
Cacna2d3	T	C	14: 28,777,934 (GRCm39)	D687G	probably damaging	Het
Ccdc136	G	A	6: 29,405,940 (GRCm39)	M95I	probably benign	Het
Cdk12	T	A	11: 98,115,355 (GRCm39)	I832N	unknown	Het
Clcn2	A	C	16: 20,526,418 (GRCm39)		probably null	Het
Csrnp2	C	T	15: 100,380,574 (GRCm39)	R239Q	probably damaging	Het
Dhrs13	T	A	11: 77,927,965 (GRCm39)	D270E	probably benign	Het
Dlgap2	G	A	8: 14,793,284 (GRCm39)	G426D	probably benign	Het
Dnah8	G	A	17: 30,967,542 (GRCm39)	D2585N	probably benign	Het
Fam120a	A	G	13: 49,045,440 (GRCm39)	Y799H	probably damaging	Het
Farp1	G	A	14: 121,460,066 (GRCm39)	V112I	probably benign	Het
Fhip2a	A	G	19: 57,367,177 (GRCm39)	D240G	probably benign	Het
Fsip2	A	G	2: 82,816,776 (GRCm39)	I4170V	probably benign	Het
Gm12185	A	G	11: 48,806,531 (GRCm39)	V220A	probably benign	Het
Gpr37l1	T	C	1: 135,094,860 (GRCm39)	Y128C	probably damaging	Het
Gsto2	A	T	19: 47,860,227 (GRCm39)	R7*	probably null	Het
Itih3	C	T	14: 30,631,430 (GRCm39)	G822D	probably benign	Het
Kcnu1	A	T	8: 26,403,673 (GRCm39)	D728V	probably damaging	Het
Lnpep	G	A	17: 17,750,758 (GRCm39)	T976I	probably damaging	Het
Map1b	A	C	13: 99,562,449 (GRCm39)	H2420Q	unknown	Het
Mc1r	A	G	8: 124,134,435 (GRCm39)	K63E	probably damaging	Het
Mpped1	G	A	15: 83,720,584 (GRCm39)	V15M	probably damaging	Het
Ncor1	T	C	11: 62,264,272 (GRCm39)	T103A	probably benign	Het
Nhsl1	A	T	10: 18,407,062 (GRCm39)	T1399S	probably benign	Het
Nlrc5	C	T	8: 95,216,996 (GRCm39)	T995M	probably benign	Het
Nrbp1	G	A	5: 31,403,190 (GRCm39)		probably null	Het
Or10g9	A	C	9: 39,912,493 (GRCm39)	F10C	probably damaging	Het
Or4c116	G	T	2: 88,942,640 (GRCm39)	T72N	possibly damaging	Het
Or8k27	T	C	2: 86,275,580 (GRCm39)	T249A	probably benign	Het
Pcdhb13	T	C	18: 37,576,663 (GRCm39)	L347P	probably damaging	Het
Pkhd1	T	C	1: 20,128,563 (GRCm39)	T4047A	probably benign	Het
Prrt2	T	A	7: 126,618,769 (GRCm39)	D232V	probably damaging	Het
Psmd5	A	C	2: 34,746,545 (GRCm39)	M344R	probably benign	Het
Pwp1	G	A	10: 85,720,397 (GRCm39)	E345K	probably damaging	Het
Qsox1	A	G	1: 155,666,851 (GRCm39)	Y213H	probably benign	Het
Rmc1	A	G	18: 12,309,203 (GRCm39)	N92D	possibly damaging	Het
Sclt1	T	C	3: 41,685,337 (GRCm39)	R39G	unknown	Het
Syne1	A	T	10: 5,093,285 (GRCm39)		probably null	Het
Tmem163	G	T	1: 127,479,078 (GRCm39)	A147E	probably damaging	Het
Trav13n-4	A	T	14: 53,601,557 (GRCm39)	M109L	probably benign	Het
Trp53bp1	T	C	2: 121,039,790 (GRCm39)	E1283G	probably damaging	Het
Trpm6	T	A	19: 18,855,129 (GRCm39)	D1929E	probably damaging	Het
Upb1	A	T	10: 75,273,978 (GRCm39)	D335V	probably damaging	Het
Vps26b	T	C	9: 26,924,104 (GRCm39)	E213G	probably damaging	Het
Vwc2	C	T	11: 11,104,215 (GRCm39)	T249I	probably benign	Het
Wwc2	A	G	8: 48,353,826 (GRCm39)	Y103H	possibly damaging	Het
Zan	A	G	5: 137,391,409 (GRCm39)	C4692R	unknown	Het
Zfp106	T	C	2: 120,369,935 (GRCm39)	E29G	probably damaging	Het
Zfp551	G	A	7: 12,150,767 (GRCm39)	A214V	possibly damaging	Het
Zfp981	T	A	4: 146,622,363 (GRCm39)	H429Q	probably benign	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
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'- ATAGGAATCTCGGGCACGTC -3'
(R):5'- ACGTGATCTTCACTCTAACCGG -3'

Sequencing Primer
(F):5'- ACGTCTCGGGACCATGG -3'
(R):5'- GGTTTCATCTTCATTAACCCCAATG -3'

Posted On

2018-08-29