Mutagenetix > Incidental Mutation

Incidental Mutation 'R6415:Khdc4'

517848

Institutional Source

Beutler Lab

Gene Symbol

Khdc4

Ensembl Gene

ENSMUSG00000028060

Gene Name

KH domain containing 4, pre-mRNA splicing factor

Synonyms

2810403A07Rik

MMRRC Submission

044557-MU

Accession Numbers

Essential gene?

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

Stock #

R6415 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

88593110-88620231 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 88607279 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 328 (F328L)

Ref Sequence

ENSEMBL: ENSMUSP00000142760 (fasta)

Gene Model

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

AlphaFold

Q3TCX3

Predicted Effect

probably benign
Transcript: ENSMUST00000029696
AA Change: F328L

PolyPhen 2 Score 0.207 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000029696
Gene: ENSMUSG00000028060
AA Change: F328L

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: ENSMUST00000197300

Predicted Effect

probably benign
Transcript: ENSMUST00000198042
AA Change: F328L

PolyPhen 2 Score 0.207 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000142773
Gene: ENSMUSG00000028060
AA Change: F328L

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
AA Change: F328L

PolyPhen 2 Score 0.249 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000142760
Gene: ENSMUSG00000028060
AA Change: F328L

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
AA Change: F328L

PolyPhen 2 Score 0.207 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000142353
Gene: ENSMUSG00000028060
AA Change: F328L

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: ENSMUST00000200438

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 97.8%
20x: 93.1%

Validation Efficiency

100% (65/65)

Allele List at MGI

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930563M21Rik	G	A	9: 55,881,296 (GRCm39)	T482M	probably benign	Het
Adam9	A	G	8: 25,468,498 (GRCm39)	Y513H	probably damaging	Het
Adamts20	C	T	15: 94,222,540 (GRCm39)		probably null	Het
B3gnt5	A	G	16: 19,588,759 (GRCm39)	D326G	probably damaging	Het
Cacna1g	A	G	11: 94,354,243 (GRCm39)	I224T	probably damaging	Het
Ccdc18	A	G	5: 108,309,612 (GRCm39)	I402M	probably benign	Het
Cckar	A	T	5: 53,860,398 (GRCm39)	C73S	probably damaging	Het
Cdk13	C	T	13: 17,913,739 (GRCm39)	R880H	probably damaging	Het
Col1a1	A	G	11: 94,830,986 (GRCm39)	N218D	unknown	Het
Csnk1g2	T	C	10: 80,474,130 (GRCm39)	I145T	possibly damaging	Het
Cul5	T	C	9: 53,557,983 (GRCm39)	D207G	probably benign	Het
Cyp2c69	A	G	19: 39,831,365 (GRCm39)	F483L	probably benign	Het
Ddx60	A	G	8: 62,436,939 (GRCm39)	D963G	probably benign	Het
Dhx8	G	T	11: 101,628,513 (GRCm39)	A142S	unknown	Het
Dock7	C	T	4: 98,880,685 (GRCm39)	R926Q	probably damaging	Het
Dscaml1	C	T	9: 45,594,975 (GRCm39)	Q693*	probably null	Het
Dysf	G	A	6: 84,117,024 (GRCm39)	C1234Y	probably damaging	Het
Ercc1	G	A	7: 19,089,102 (GRCm39)		probably null	Het
Fam91a1	T	C	15: 58,314,766 (GRCm39)	L549P	probably damaging	Het
Fxyd2	T	A	9: 45,314,592 (GRCm39)	Y5N	possibly damaging	Het
Gab1	C	A	8: 81,515,226 (GRCm39)	R364L	possibly damaging	Het
Gpr182	T	A	10: 127,586,375 (GRCm39)	D192V	possibly damaging	Het
Gps1	T	C	11: 120,678,548 (GRCm39)	V286A	possibly damaging	Het
Grk1	A	G	8: 13,463,127 (GRCm39)	Y383C	probably damaging	Het
H2bc15	T	C	13: 21,938,656 (GRCm39)	Y122H	probably benign	Het
Hic1	G	A	11: 75,057,143 (GRCm39)	P582L	possibly damaging	Het
Igkv4-61	C	A	6: 69,394,138 (GRCm39)	A31S	possibly damaging	Het
Lactb	T	C	9: 66,877,927 (GRCm39)	K301E	possibly damaging	Het
Lrp3	A	T	7: 34,903,593 (GRCm39)	V251E	probably benign	Het
Mapt	G	A	11: 104,189,824 (GRCm39)	G265S	probably benign	Het
Obscn	A	T	11: 58,925,956 (GRCm39)	D6245E	probably damaging	Het
Or10al2	G	T	17: 37,983,448 (GRCm39)	C178F	possibly damaging	Het
Or1j12	A	G	2: 36,342,617 (GRCm39)	S7G	probably damaging	Het
Or4b1c	T	A	2: 90,126,381 (GRCm39)	I275F	probably damaging	Het
Or4c10b	T	C	2: 89,711,206 (GRCm39)	L12P	probably damaging	Het
Or6c207	T	C	10: 129,104,890 (GRCm39)	T101A	probably benign	Het
Or7e165	T	A	9: 19,695,044 (GRCm39)	I205N	probably damaging	Het
Or7g19	T	C	9: 18,856,415 (GRCm39)	L157P	probably damaging	Het
Oxsm	A	T	14: 16,241,904 (GRCm38)	H288Q	probably benign	Het
Pcdh9	C	T	14: 93,253,278 (GRCm39)	M1128I	possibly damaging	Het
Pcdha8	T	C	18: 37,127,614 (GRCm39)	Y699H	probably damaging	Het
Pgk2	A	T	17: 40,518,459 (GRCm39)	I323N	probably benign	Het
Plin4	A	G	17: 56,410,264 (GRCm39)	V1216A	probably damaging	Het
Ppargc1a	T	C	5: 51,620,176 (GRCm39)		probably benign	Het
Prelp	A	T	1: 133,840,516 (GRCm39)	I322N	probably benign	Het
Prelp	A	T	1: 133,842,395 (GRCm39)	I250N	probably damaging	Het
Prss27	T	A	17: 24,261,882 (GRCm39)	C63*	probably null	Het
Rab38	G	A	7: 88,079,748 (GRCm39)	A47T	possibly damaging	Het
Rprd2	G	A	3: 95,681,531 (GRCm39)	A436V	probably benign	Het
Sacs	A	T	14: 61,442,808 (GRCm39)	N1618I	probably damaging	Het
Scp2	T	G	4: 107,962,337 (GRCm39)	S63R	probably benign	Het
Sftpb	T	G	6: 72,281,633 (GRCm39)	W9G	probably damaging	Het
Slco1a4	A	T	6: 141,780,415 (GRCm39)	L125*	probably null	Het
Sptlc1	T	C	13: 53,505,728 (GRCm39)		probably null	Het
Sub1	T	A	15: 11,986,560 (GRCm39)	M96L	probably benign	Het
Tanc1	T	C	2: 59,667,458 (GRCm39)	V1233A	probably benign	Het
Tmem140	A	T	6: 34,849,658 (GRCm39)	D58V	probably damaging	Het
Tmem231	G	A	8: 112,653,524 (GRCm39)		probably benign	Het
Tpt1	T	C	14: 76,083,811 (GRCm39)	Y91H	probably benign	Het
Trap1	C	T	16: 3,861,856 (GRCm39)	R636H	possibly damaging	Het
Ttc14	A	G	3: 33,857,724 (GRCm39)	H275R	possibly damaging	Het
Tut7	T	A	13: 59,964,110 (GRCm39)		probably null	Het
Vps35l	T	C	7: 118,391,869 (GRCm39)	W494R	probably damaging	Het
Ypel1	A	G	16: 16,921,438 (GRCm39)		probably null	Het
Zbtb44	T	A	9: 30,975,510 (GRCm39)	I380N	possibly damaging	Het
Zswim5	T	C	4: 116,838,063 (GRCm39)	F798L	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
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
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'- TGACTTTGTGCTCCAGATTGAG -3'
(R):5'- GATAAACACCACGGTTAAGAATGGC -3'

Sequencing Primer
(F):5'- TGCTCCAGATTGAGTAGTTTGG -3'
(R):5'- ACCACGGTTAAGAATGGCTTTCC -3'

Posted On

2018-05-24