Mutagenetix > Incidental Mutation

Incidental Mutation 'R1523:Khdc3'

167643

Institutional Source

Beutler Lab

Gene Symbol

Khdc3

Ensembl Gene

ENSMUSG00000092622

Gene Name

KH domain containing 3, subcortical maternal complex member

Synonyms

FILIA, ecat1, 2410004A20Rik

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.097) question?

Stock #

R1523 (G1)

Quality Score

Status

Not validated

Chromosome

Chromosomal Location

73009118-73011720 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 73010773 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Lysine at position 208 (E208K)

Ref Sequence

ENSEMBL: ENSMUSP00000133915 (fasta)

Gene Model

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

AlphaFold

Q9CWU5

Predicted Effect

possibly damaging
Transcript: ENSMUST00000034737
AA Change: E208K

PolyPhen 2 Score 0.528 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000034737
Gene: ENSMUSG00000092622
AA Change: E208K

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: E184K

PolyPhen 2 Score 0.400 (Sensitivity: 0.89; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000132527
Gene: ENSMUSG00000092622
AA Change: E184K

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: E208K

PolyPhen 2 Score 0.528 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000133915
Gene: ENSMUSG00000092622
AA Change: E208K

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: 99.2%
3x: 98.3%
10x: 96.3%
20x: 92.9%

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700020L24Rik	G	T	11: 83,331,232 (GRCm39)	E48*	probably null	Het
4930503B20Rik	A	G	3: 146,356,864 (GRCm39)	S15P	probably damaging	Het
5530400C23Rik	A	G	6: 133,271,256 (GRCm39)	E100G	possibly damaging	Het
Abcg2	T	C	6: 58,662,679 (GRCm39)	F507S	possibly damaging	Het
Adgrf5	A	T	17: 43,761,044 (GRCm39)	Q913L	probably benign	Het
Ak7	A	T	12: 105,732,867 (GRCm39)	N537I	probably benign	Het
Anks1	T	A	17: 28,270,629 (GRCm39)		probably null	Het
Arhgap32	T	A	9: 32,168,048 (GRCm39)	V677D	probably damaging	Het
Ark2c	G	A	18: 77,550,634 (GRCm39)	T98I	probably benign	Het
Arnt	C	T	3: 95,396,965 (GRCm39)	P466L	possibly damaging	Het
Arrb1	T	G	7: 99,243,872 (GRCm39)	L274R	probably damaging	Het
Atf2	A	T	2: 73,693,552 (GRCm39)	D3E	probably damaging	Het
Baz2b	C	T	2: 59,798,981 (GRCm39)	R381Q	possibly damaging	Het
Cacna1g	C	T	11: 94,333,555 (GRCm39)		probably null	Het
Ccr10	C	T	11: 101,064,501 (GRCm39)	R343Q	probably damaging	Het
Clca3a2	G	T	3: 144,777,405 (GRCm39)	S822*	probably null	Het
Col12a1	A	T	9: 79,568,278 (GRCm39)	Y1649N	probably benign	Het
Col23a1	G	A	11: 51,452,743 (GRCm39)		probably null	Het
Cp	T	C	3: 20,043,229 (GRCm39)	Y1006H	probably benign	Het
Ctbs	A	G	3: 146,160,735 (GRCm39)	T101A	probably benign	Het
Cyp4a31	T	C	4: 115,426,951 (GRCm39)	F170L	probably benign	Het
Dock1	A	C	7: 134,345,976 (GRCm39)	I173L	possibly damaging	Het
Dock4	A	G	12: 40,743,024 (GRCm39)	D393G	possibly damaging	Het
Dsg1a	T	A	18: 20,455,374 (GRCm39)	S113T	probably damaging	Het
Epha3	T	C	16: 63,431,311 (GRCm39)	D530G	probably damaging	Het
Erbb4	T	A	1: 68,435,411 (GRCm39)	H162L	possibly damaging	Het
Fam131c	C	T	4: 141,110,142 (GRCm39)	T180I	probably benign	Het
Fndc1	A	G	17: 7,992,041 (GRCm39)	S552P	unknown	Het
Foxf1	A	G	8: 121,811,297 (GRCm39)		probably null	Het
Frem2	T	C	3: 53,562,828 (GRCm39)	T560A	possibly damaging	Het
Gabra4	G	A	5: 71,790,975 (GRCm39)	T289M	probably damaging	Het
Gcnt1	A	G	19: 17,307,197 (GRCm39)	V176A	probably damaging	Het
Gemin8	G	A	X: 164,963,644 (GRCm39)	S100N	probably benign	Het
Gm1527	T	C	3: 28,974,567 (GRCm39)	I460T	probably damaging	Het
Gm6729	A	G	10: 86,376,039 (GRCm39)		noncoding transcript	Het
Gprin2	T	C	14: 33,917,036 (GRCm39)	S245G	probably benign	Het
Gsdmc	A	T	15: 63,675,479 (GRCm39)	I112N	probably damaging	Het
Hspb6	A	G	7: 30,252,848 (GRCm39)	D30G	probably benign	Het
Hydin	A	G	8: 111,259,903 (GRCm39)	D2625G	probably benign	Het
Iqca1	C	A	1: 90,070,453 (GRCm39)	G133V	probably null	Het
Irf2	T	A	8: 47,290,875 (GRCm39)		probably null	Het
Kdm3b	T	C	18: 34,926,226 (GRCm39)		probably null	Het
Kifc1	A	T	17: 34,102,636 (GRCm39)	S263T	probably benign	Het
Lrig3	C	A	10: 125,844,567 (GRCm39)	T677K	probably damaging	Het
Magec2	T	A	X: 61,334,512 (GRCm39)	D177E	probably benign	Het
Mapkapk3	A	T	9: 107,140,822 (GRCm39)		probably null	Het
Mertk	T	C	2: 128,632,248 (GRCm39)		probably null	Het
Metrn	A	G	17: 26,013,951 (GRCm39)	*292R	probably null	Het
Mllt6	G	T	11: 97,555,849 (GRCm39)	A60S	probably damaging	Het
Mmp21	T	C	7: 133,280,774 (GRCm39)	I65M	probably benign	Het
Myo7b	A	G	18: 32,099,929 (GRCm39)	L1651P	probably damaging	Het
Nhsl1	A	G	10: 18,284,103 (GRCm39)	S15G	probably benign	Het
Nos1ap	T	C	1: 170,165,687 (GRCm39)	D192G	probably benign	Het
Nrcam	A	G	12: 44,619,032 (GRCm39)	T844A	probably damaging	Het
Pax4	A	G	6: 28,444,840 (GRCm39)	L203P	probably damaging	Het
Pbld2	T	C	10: 62,912,212 (GRCm39)	I280T	probably benign	Het
Pclo	A	G	5: 14,838,420 (GRCm39)	Y4681C	unknown	Het
Phyhip	T	A	14: 70,699,200 (GRCm39)	M1K	probably null	Het
Plppr4	T	C	3: 117,116,490 (GRCm39)	N456D	probably damaging	Het
Prpf31	T	C	7: 3,643,856 (GRCm39)	Y473H	probably damaging	Het
Rapgef2	A	T	3: 79,000,056 (GRCm39)	V564D	probably damaging	Het
Rexo1	T	C	10: 80,378,585 (GRCm39)	S1123G	probably benign	Het
Rnasel	C	A	1: 153,631,759 (GRCm39)	Q513K	probably damaging	Het
Rnf213	T	C	11: 119,332,714 (GRCm39)	V2641A	probably damaging	Het
Rnf40	G	T	7: 127,189,787 (GRCm39)	R184L	probably damaging	Het
Rnf8	A	G	17: 29,845,946 (GRCm39)	K179R	probably damaging	Het
Sipa1l2	C	T	8: 126,174,352 (GRCm39)	D1309N	possibly damaging	Het
Slc25a38	T	A	9: 119,952,769 (GRCm39)	M307K	possibly damaging	Het
Snx33	T	C	9: 56,833,466 (GRCm39)	D201G	possibly damaging	Het
Sulf1	T	A	1: 12,887,574 (GRCm39)	Y249*	probably null	Het
Sult2a4	G	A	7: 13,643,785 (GRCm39)	Q261*	probably null	Het
Syndig1	G	A	2: 149,845,154 (GRCm39)	A226T	probably damaging	Het
Tcaf2	C	T	6: 42,601,385 (GRCm39)	W891*	probably null	Het
Tcf15	C	A	2: 151,985,808 (GRCm39)	T88K	probably damaging	Het
Tmem19	A	T	10: 115,183,122 (GRCm39)	M117K	probably damaging	Het
Trim32	T	C	4: 65,532,241 (GRCm39)	L266P	probably benign	Het
Vmn2r11	T	C	5: 109,201,707 (GRCm39)	I266V	probably benign	Het
Vmn2r73	A	T	7: 85,519,486 (GRCm39)	Y491N	probably benign	Het
Wrn	C	T	8: 33,782,744 (GRCm39)	E486K	probably benign	Het
Zfp457	T	C	13: 67,441,501 (GRCm39)	E262G	probably damaging	Het
Zfp598	A	G	17: 24,897,603 (GRCm39)	D308G	probably null	Het
Zup1	T	C	10: 33,803,436 (GRCm39)	I549M	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
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
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'- TTCCGTGAAGGTCCCTGAGACG -3'
(R):5'- TGTGCTGGGCAAAGGCTTCATC -3'

Sequencing Primer
(F):5'- GTCCCTGAGACGGCCAC -3'
(R):5'- TAGTATCAGTGGCCTCCACG -3'

Posted On

2014-04-13