Mutagenetix > Incidental Mutation

Incidental Mutation 'R5153:Khdc3'

395531

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

042735-MU

Accession Numbers

Essential gene?

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

Stock #

R5153 (G1)

Quality Score

102

Status

Not validated

Chromosome

Chromosomal Location

73009118-73011720 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 73010720 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Arginine at position 190 (Q190R)

Ref Sequence

ENSEMBL: ENSMUSP00000133915 (fasta)

Gene Model

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

AlphaFold

Q9CWU5

Predicted Effect

probably benign
Transcript: ENSMUST00000034737
AA Change: Q190R

PolyPhen 2 Score 0.177 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000034737
Gene: ENSMUSG00000092622
AA Change: Q190R

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

probably benign
Transcript: ENSMUST00000167514
AA Change: Q166R

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000132527
Gene: ENSMUSG00000092622
AA Change: Q166R

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

probably benign
Transcript: ENSMUST00000173734
AA Change: Q190R

PolyPhen 2 Score 0.177 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000133915
Gene: ENSMUSG00000092622
AA Change: Q190R

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

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.3%
20x: 95.2%

Validation Efficiency

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2300003K06Rik	A	T	11: 99,728,073 (GRCm39)	C257S	unknown	Het
4930596D02Rik	C	A	14: 35,532,212 (GRCm39)	R121L	probably benign	Het
Aadacl4fm1	T	A	4: 144,248,837 (GRCm39)	M68K	probably benign	Het
Acin1	A	G	14: 54,883,070 (GRCm39)	V194A	probably benign	Het
Acsm1	T	C	7: 119,239,950 (GRCm39)	I298T	possibly damaging	Het
Aoc1	A	G	6: 48,885,681 (GRCm39)	N729D	probably benign	Het
Apobr	C	T	7: 126,186,904 (GRCm39)	T20I	possibly damaging	Het
Arsb	A	G	13: 94,077,106 (GRCm39)	E491G	probably benign	Het
AW209491	C	G	13: 14,811,764 (GRCm39)	Q206E	probably benign	Het
Camsap1	A	T	2: 25,823,630 (GRCm39)	N1473K	probably damaging	Het
Casp8	A	G	1: 58,884,004 (GRCm39)	Q457R	probably benign	Het
Ccdc154	G	A	17: 25,387,315 (GRCm39)	A350T	probably damaging	Het
Cecr2	A	G	6: 120,711,521 (GRCm39)	E183G	probably benign	Het
Cep295	A	T	9: 15,268,925 (GRCm39)	S39T	probably benign	Het
Cep350	A	T	1: 155,811,692 (GRCm39)	I416K	probably damaging	Het
Cidea	C	T	18: 67,500,490 (GRCm39)	T184M	probably damaging	Het
Cnot10	G	A	9: 114,442,803 (GRCm39)	A468V	probably damaging	Het
Cstdc1	A	G	2: 148,625,360 (GRCm39)	Q98R	probably benign	Het
Defb22	A	T	2: 152,327,722 (GRCm39)	N154K	unknown	Het
Dnah17	A	T	11: 117,973,800 (GRCm39)	C1915*	probably null	Het
Dnah2	T	C	11: 69,411,759 (GRCm39)	T288A	possibly damaging	Het
Dop1b	T	A	16: 93,570,891 (GRCm39)	M1512K	probably damaging	Het
Dsp	T	G	13: 38,366,282 (GRCm39)	I572S	probably damaging	Het
Eepd1	A	G	9: 25,498,049 (GRCm39)	H378R	probably benign	Het
Elapor1	A	T	3: 108,380,063 (GRCm39)	Y349N	possibly damaging	Het
Emilin2	A	G	17: 71,580,497 (GRCm39)	M743T	possibly damaging	Het
Ext1	C	A	15: 52,939,213 (GRCm39)	W612L	probably damaging	Het
F2rl2	A	G	13: 95,833,620 (GRCm39)	T17A	probably benign	Het
Fbxl8	T	G	8: 105,993,739 (GRCm39)	C32G	probably damaging	Het
Fbxw17	A	G	13: 50,573,897 (GRCm39)	T38A	probably damaging	Het
Flii	A	T	11: 60,607,512 (GRCm39)	L882Q	possibly damaging	Het
Focad	T	G	4: 88,278,121 (GRCm39)	S1197A	unknown	Het
H1f11-ps	A	G	19: 47,159,356 (GRCm39)	V73A	probably damaging	Het
Heatr5b	G	A	17: 79,102,536 (GRCm39)	R1281*	probably null	Het
Krt9	T	A	11: 100,082,068 (GRCm39)	D244V	probably damaging	Het
Ldhd	T	C	8: 112,353,724 (GRCm39)	E463G	probably benign	Het
Lig4	A	T	8: 10,023,003 (GRCm39)	V259E	possibly damaging	Het
Luc7l3	A	T	11: 94,186,806 (GRCm39)		probably benign	Het
Man1a2	T	C	3: 100,563,579 (GRCm39)	E22G	probably damaging	Het
Mmp23	T	G	4: 155,735,797 (GRCm39)	D258A	probably damaging	Het
Msantd2	C	T	9: 37,434,509 (GRCm39)	R250*	probably null	Het
Mynn	T	C	3: 30,665,738 (GRCm39)	S457P	probably benign	Het
Nectin1	C	T	9: 43,714,795 (GRCm39)	H50Y	probably damaging	Het
Or10a3b	T	C	7: 108,444,906 (GRCm39)	I104V	probably benign	Het
Or2d3c	C	T	7: 106,525,776 (GRCm39)	V297M	possibly damaging	Het
Or4a47	G	A	2: 89,665,578 (GRCm39)	T237I	possibly damaging	Het
Or6c6c	A	G	10: 129,541,026 (GRCm39)	N93S	probably benign	Het
Pfkfb2	G	A	1: 130,629,527 (GRCm39)	T303M	probably damaging	Het
Pkhd1l1	A	G	15: 44,368,705 (GRCm39)	D841G	probably benign	Het
Plxna4	A	T	6: 32,201,094 (GRCm39)		probably null	Het
Podnl1	C	T	8: 84,857,272 (GRCm39)	H294Y	probably benign	Het
Ppig	T	A	2: 69,579,994 (GRCm39)	D509E	unknown	Het
Ppp1r16a	T	A	15: 76,578,596 (GRCm39)	Y433*	probably null	Het
Prdm1	A	C	10: 44,326,221 (GRCm39)	V134G	possibly damaging	Het
Prx	T	C	7: 27,217,901 (GRCm39)	S940P	probably damaging	Het
Ptprd	C	T	4: 75,930,339 (GRCm39)	V731I	probably damaging	Het
Qki	A	G	17: 10,457,820 (GRCm39)		probably null	Het
Rassf6	T	C	5: 90,754,699 (GRCm39)	K206R	possibly damaging	Het
Rdh16f2	G	A	10: 127,712,124 (GRCm39)	E194K	possibly damaging	Het
Rims1	C	A	1: 22,522,328 (GRCm39)	G457*	probably null	Het
Ripk1	T	G	13: 34,197,279 (GRCm39)	I123R	probably damaging	Het
Rnf111	A	T	9: 70,383,422 (GRCm39)	S170R	probably benign	Het
Shc3	A	T	13: 51,615,413 (GRCm39)	F181L	probably damaging	Het
Siglec1	A	C	2: 130,927,497 (GRCm39)	V103G	probably damaging	Het
Slc26a11	G	T	11: 119,268,085 (GRCm39)	A488S	possibly damaging	Het
Smoc2	A	T	17: 14,556,841 (GRCm39)	T97S	probably damaging	Het
Son	T	C	16: 91,451,910 (GRCm39)	I219T	possibly damaging	Het
Sptbn1	A	T	11: 30,071,510 (GRCm39)	I1474N	possibly damaging	Het
Syt16	A	T	12: 74,269,542 (GRCm39)	D127V	possibly damaging	Het
Tet1	G	T	10: 62,714,357 (GRCm39)	N479K	possibly damaging	Het
Thsd7a	G	A	6: 12,338,654 (GRCm39)	A1192V	probably benign	Het
Tmed3	G	A	9: 89,581,825 (GRCm39)	R213*	probably null	Het
Traj57	A	G	14: 54,396,016 (GRCm39)		probably benign	Het
Trpv1	G	T	11: 73,129,342 (GRCm39)	R86S	probably benign	Het
Usp48	T	A	4: 137,343,673 (GRCm39)	F434L	possibly damaging	Het
Vmn2r59	A	C	7: 41,691,834 (GRCm39)		probably null	Het
Vmn2r71	T	A	7: 85,268,430 (GRCm39)	I211N	possibly damaging	Het
Vps13b	T	A	15: 35,422,599 (GRCm39)	D186E	probably damaging	Het
Vps33a	A	G	5: 123,696,691 (GRCm39)	S321P	probably damaging	Het
Wdr12	A	T	1: 60,133,670 (GRCm39)	D19E	probably benign	Het
Zc3h12c	A	G	9: 52,037,947 (GRCm39)	F278L	probably damaging	Het
Zpld1	T	C	16: 55,067,007 (GRCm39)	T183A	probably damaging	Het
Zswim2	G	T	2: 83,770,010 (GRCm39)	T68K	possibly 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
R5261:Khdc3	UTSW	9	73,010,768 (GRCm39)	missense	possibly damaging	0.92
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'- TTCCAACTCAGTAGAGGCTCTGG -3'
(R):5'- ACCTTCACAGGAGCCAACTG -3'

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

Posted On

2016-06-21