Mutagenetix > Incidental Mutation

Incidental Mutation 'R5261:Khdc3'

401444

Institutional Source

Beutler Lab

Gene Symbol

Khdc3

Ensembl Gene

ENSMUSG00000092622

Gene Name

KH domain containing 3, subcortical maternal complex member

Synonyms

FILIA, ecat1, 2410004A20Rik

MMRRC Submission

042830-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.094) question?

Stock #

R5261 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

73009118-73011720 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 73010768 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glycine at position 182 (V182G)

Ref Sequence

ENSEMBL: ENSMUSP00000132527 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000034737] [ENSMUST00000167514] [ENSMUST00000172578] [ENSMUST00000173734] [ENSMUST00000174203]

AlphaFold

Q9CWU5

Predicted Effect

possibly damaging
Transcript: ENSMUST00000034737
AA Change: V206G

PolyPhen 2 Score 0.861 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000034737
Gene: ENSMUSG00000092622
AA Change: V206G

Domain	Start	End	E-Value	Type
Pfam:MOEP19	28	113	4.5e-34	PFAM
internal_repeat_1	117	217	6.81e-11	PROSPERO
internal_repeat_1	218	316	6.81e-11	PROSPERO
internal_repeat_2	275	397	3.62e-8	PROSPERO

Predicted Effect

possibly damaging
Transcript: ENSMUST00000167514
AA Change: V182G

PolyPhen 2 Score 0.915 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000132527
Gene: ENSMUSG00000092622
AA Change: V182G

Domain	Start	End	E-Value	Type
internal_repeat_1	117	212	2.21e-8	PROSPERO
internal_repeat_1	207	356	2.21e-8	PROSPERO

Predicted Effect

probably benign
Transcript: ENSMUST00000172578

SMART Domains

Protein: ENSMUSP00000133850
Gene: ENSMUSG00000092622

Domain	Start	End	E-Value	Type
PDB:3V69\|B	1	75	4e-49	PDB

Predicted Effect

possibly damaging
Transcript: ENSMUST00000173734
AA Change: V206G

PolyPhen 2 Score 0.861 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000133915
Gene: ENSMUSG00000092622
AA Change: V206G

Domain	Start	End	E-Value	Type
internal_repeat_2	116	194	1.27e-8	PROSPERO
internal_repeat_1	117	231	1.6e-13	PROSPERO
internal_repeat_1	231	341	1.6e-13	PROSPERO
internal_repeat_2	267	344	1.27e-8	PROSPERO

Predicted Effect

probably benign
Transcript: ENSMUST00000174203

SMART Domains

Protein: ENSMUSP00000134473
Gene: ENSMUSG00000092310

Domain	Start	End	E-Value	Type
internal_repeat_1	116	173	5.47e-9	PROSPERO
internal_repeat_1	177	233	5.47e-9	PROSPERO

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.5%
20x: 93.1%

Validation Efficiency

96% (64/67)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene belongs to the KHDC1 family, members of which contain an atypical KH domain that may not bind RNA like canonical KH domains. This gene is specifically expressed in the oocytes, and recent studies suggest that it may function as a regulator of genomic imprinting in the oocyte. Mutations in this gene are associated with recurrent biparental complete hydatidiform mole. [provided by RefSeq, Dec 2011]
PHENOTYPE: Homozygous null mice display a maternal effect defect in embryogenesis with delayed embryonic development and spindle abnormalities resulting in decreased litter sizes for homozygous females. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
6820408C15Rik	C	G	2: 152,282,777 (GRCm39)	P211A	probably damaging	Het
Ambra1	G	A	2: 91,715,951 (GRCm39)	V761M	probably damaging	Het
Amfr	T	A	8: 94,702,798 (GRCm39)		probably null	Het
Asphd1	C	A	7: 126,545,287 (GRCm39)	A357S	probably benign	Het
Brd3	C	A	2: 27,353,931 (GRCm39)	Q60H	probably damaging	Het
Cd96	T	A	16: 45,890,016 (GRCm39)	M336L	probably benign	Het
Cep152	T	A	2: 125,406,125 (GRCm39)	H1469L	probably benign	Het
Coro1a	G	T	7: 126,299,816 (GRCm39)		probably null	Het
D630045J12Rik	A	T	6: 38,171,555 (GRCm39)	L871Q	probably benign	Het
Depdc5	C	T	5: 33,095,635 (GRCm39)	P824L	probably damaging	Het
Enpep	T	G	3: 129,099,075 (GRCm39)	D467A	probably damaging	Het
Extl2	G	A	3: 115,821,013 (GRCm39)	A273T	probably benign	Het
Foxi3	T	A	6: 70,937,500 (GRCm39)	F218Y	probably damaging	Het
Golga2	A	G	2: 32,194,166 (GRCm39)	M521V	probably benign	Het
Gpr142	T	A	11: 114,695,168 (GRCm39)	N44K	probably damaging	Het
Gtf2ird2	A	G	5: 134,245,061 (GRCm39)	I440V	probably benign	Het
Gucy1b2	T	A	14: 62,642,028 (GRCm39)	K698I	probably damaging	Het
Hspa1b	T	C	17: 35,177,983 (GRCm39)	M1V	probably null	Het
Ints9	T	A	14: 65,245,521 (GRCm39)	Y260N	probably benign	Het
Ky	A	G	9: 102,414,798 (GRCm39)		probably null	Het
Map2k1	T	A	9: 64,098,843 (GRCm39)	I263F	probably damaging	Het
Or13a18	A	C	7: 140,190,576 (GRCm39)	I166L	probably benign	Het
Or2t47	T	C	11: 58,442,877 (GRCm39)	S63G	probably benign	Het
Or5ak25	A	G	2: 85,269,241 (GRCm39)	V87A	probably benign	Het
Otogl	T	A	10: 107,613,453 (GRCm39)	H2004L	probably benign	Het
Palmd	T	C	3: 116,717,009 (GRCm39)	H496R	probably benign	Het
Papolb	C	G	5: 142,515,409 (GRCm39)	R78P	possibly damaging	Het
Pcdh10	G	A	3: 45,336,247 (GRCm39)	G854R	probably damaging	Het
Pdcd11	A	G	19: 47,101,976 (GRCm39)	I1054V	probably benign	Het
Pik3ap1	A	T	19: 41,364,545 (GRCm39)	L58Q	probably damaging	Het
Ppp2ca	A	G	11: 51,989,937 (GRCm39)	K21R	probably benign	Het
Prmt5	A	C	14: 54,745,373 (GRCm39)	I598S	probably damaging	Het
Pycr1	T	A	11: 120,532,050 (GRCm39)	I239F	probably damaging	Het
R3hdm2	C	T	10: 127,334,285 (GRCm39)	R896C	probably damaging	Het
Rev3l	C	T	10: 39,722,725 (GRCm39)	P699S	probably damaging	Het
Samd1	CGAGGAGGAGGAGGAGGAGGA	CGAGGAGGAGGAGGAGGA	8: 84,725,625 (GRCm39)		probably benign	Het
Sel1l	A	T	12: 91,791,658 (GRCm39)	M351K	possibly damaging	Het
Sesn2	A	G	4: 132,226,617 (GRCm39)	L159P	probably damaging	Het
Slc35f4	T	A	14: 49,540,946 (GRCm39)		probably benign	Het
Slc3a1	C	A	17: 85,359,403 (GRCm39)	N409K	probably damaging	Het
Slc45a2	C	T	15: 11,027,871 (GRCm39)	T480I	probably damaging	Het
Slco1c1	T	C	6: 141,492,502 (GRCm39)	F246S	probably damaging	Het
Socs2	T	G	10: 95,228,681 (GRCm39)	I190L	unknown	Het
Srsf1	T	A	11: 87,938,684 (GRCm39)	I7N	possibly damaging	Het
Stox1	T	A	10: 62,503,620 (GRCm39)	H145L	probably damaging	Het
Trap1	A	T	16: 3,874,286 (GRCm39)	I243N	probably damaging	Het
Trav7-3	T	C	14: 53,681,207 (GRCm39)	I83T	probably benign	Het
Trmt9b	T	C	8: 36,979,078 (GRCm39)	I227T	probably benign	Het
Tuft1	A	T	3: 94,546,712 (GRCm39)	I42K	possibly damaging	Het
Umps	A	G	16: 33,787,344 (GRCm39)	V3A	probably benign	Het
Vim	A	C	2: 13,579,643 (GRCm39)	E134A	probably null	Het
Vmn1r28	C	A	6: 58,242,524 (GRCm39)	H122Q	probably benign	Het
Vps51	T	G	19: 6,121,063 (GRCm39)	E283D	probably benign	Het
Vsig10l	T	A	7: 43,120,274 (GRCm39)	V760D	probably damaging	Het
Xrn1	A	G	9: 95,927,596 (GRCm39)	D1460G	probably benign	Het
Zfp282	A	G	6: 47,874,824 (GRCm39)	D343G	probably damaging	Het
Zfp35	A	G	18: 24,136,778 (GRCm39)	H374R	probably damaging	Het

Other mutations in Khdc3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02987:Khdc3	APN	9	73,009,948 (GRCm39)	missense	possibly damaging	0.56
R1487:Khdc3	UTSW	9	73,009,846 (GRCm39)	missense	probably benign	0.19
R1523:Khdc3	UTSW	9	73,010,773 (GRCm39)	missense	possibly damaging	0.53
R1545:Khdc3	UTSW	9	73,010,942 (GRCm39)	missense	probably benign	0.05
R1951:Khdc3	UTSW	9	73,010,519 (GRCm39)	missense	possibly damaging	0.48
R2935:Khdc3	UTSW	9	73,010,987 (GRCm39)	missense	possibly damaging	0.92
R3076:Khdc3	UTSW	9	73,010,212 (GRCm39)	missense	probably damaging	1.00
R3880:Khdc3	UTSW	9	73,010,872 (GRCm39)	missense	possibly damaging	0.73
R3899:Khdc3	UTSW	9	73,011,628 (GRCm39)	intron	probably benign
R3900:Khdc3	UTSW	9	73,011,628 (GRCm39)	intron	probably benign
R4224:Khdc3	UTSW	9	73,010,153 (GRCm39)	missense	possibly damaging	0.92
R4412:Khdc3	UTSW	9	73,010,156 (GRCm39)	missense	possibly damaging	0.93
R4529:Khdc3	UTSW	9	73,011,301 (GRCm39)	missense	possibly damaging	0.83
R4647:Khdc3	UTSW	9	73,009,868 (GRCm39)	missense	possibly damaging	0.81
R4648:Khdc3	UTSW	9	73,009,868 (GRCm39)	missense	possibly damaging	0.81
R5153:Khdc3	UTSW	9	73,010,720 (GRCm39)	missense	probably benign	0.18
R8362:Khdc3	UTSW	9	73,010,848 (GRCm39)	missense	possibly damaging	0.96
X0024:Khdc3	UTSW	9	73,011,206 (GRCm39)	missense	probably benign	0.01
X0026:Khdc3	UTSW	9	73,010,265 (GRCm39)	missense	possibly damaging	0.95
X0066:Khdc3	UTSW	9	73,011,463 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- TTTCTTCCAACTCAGTAGAGGC -3'
(R):5'- ACCTTCACAGGAGCCAACTG -3'

Sequencing Primer
(F):5'- TTCCAACTCAGTAGAGGCTCTGG -3'
(R):5'- ACCTTCACGGGAGCCAACTG -3'

Posted On

2016-07-06