Mutagenetix > Incidental Mutation

Incidental Mutation 'R1545:Khdc3'

172119

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

039584-MU

Accession Numbers

Essential gene?

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

Stock #

R1545 (G1)

Quality Score

Status

Not validated

Chromosome

Chromosomal Location

73009118-73011720 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to G at 73010942 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Arginine at position 240 (P240R)

Ref Sequence

ENSEMBL: ENSMUSP00000132527 (fasta)

Gene Model

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

AlphaFold

Q9CWU5

Predicted Effect

probably benign
Transcript: ENSMUST00000034737
AA Change: P264R

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000034737
Gene: ENSMUSG00000092622
AA Change: P264R

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: P240R

PolyPhen 2 Score 0.052 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000132527
Gene: ENSMUSG00000092622
AA Change: P240R

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: P264R

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000133915
Gene: ENSMUSG00000092622
AA Change: P264R

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

unknown
Transcript: ENSMUST00000174203
AA Change: P174R

SMART Domains

Protein: ENSMUSP00000134473
Gene: ENSMUSG00000092310
AA Change: P174R

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: 99.1%
3x: 98.2%
10x: 95.8%
20x: 90.6%

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: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aaas	C	T	15: 102,247,641 (GRCm39)	R410H	probably damaging	Het
Abca2	T	C	2: 25,332,370 (GRCm39)	C1468R	probably benign	Het
Actl9	T	A	17: 33,652,231 (GRCm39)	I97N	probably damaging	Het
Alkbh2	C	T	5: 114,262,287 (GRCm39)	E148K	probably damaging	Het
Asb3	T	A	11: 31,006,217 (GRCm39)	M234K	probably benign	Het
Bax	A	C	7: 45,111,357 (GRCm39)	H168Q	probably null	Het
Brinp1	A	G	4: 68,681,192 (GRCm39)	L446P	possibly damaging	Het
Cdc14a	A	G	3: 116,087,373 (GRCm39)		probably null	Het
Cfap299	C	A	5: 98,477,291 (GRCm39)	Q27K	probably benign	Het
Cpq	A	T	15: 33,250,146 (GRCm39)	I168F	probably damaging	Het
Crkl	A	T	16: 17,301,556 (GRCm39)	N270I	probably damaging	Het
Cul7	G	A	17: 46,962,479 (GRCm39)	E37K	probably damaging	Het
Eps15	C	T	4: 109,169,526 (GRCm39)	T112I	probably benign	Het
F5	C	T	1: 164,036,529 (GRCm39)	R1897*	probably null	Het
Fbxl5	A	T	5: 43,928,140 (GRCm39)	L40Q	probably damaging	Het
Fhip1a	C	T	3: 85,573,261 (GRCm39)	S896N	probably damaging	Het
Gprc5a	C	A	6: 135,060,459 (GRCm39)	T316K	probably damaging	Het
Hectd4	T	A	5: 121,462,019 (GRCm39)	L2299Q	possibly damaging	Het
Kif20b	A	G	19: 34,906,318 (GRCm39)	T69A	probably damaging	Het
Kptn	C	G	7: 15,857,888 (GRCm39)	Q239E	probably benign	Het
Lep	T	C	6: 29,070,831 (GRCm39)	S52P	probably damaging	Het
Lrig3	G	A	10: 125,844,416 (GRCm39)	V627M	possibly damaging	Het
Lrrc37	T	C	11: 103,499,745 (GRCm39)	K615E	probably benign	Het
Mdga1	G	A	17: 30,061,876 (GRCm39)	R792C	probably damaging	Het
Mink1	T	C	11: 70,489,717 (GRCm39)	V58A	possibly damaging	Het
Neu1	G	A	17: 35,153,374 (GRCm39)	R299Q	probably benign	Het
Nrg3	T	A	14: 38,129,111 (GRCm39)	I375F	probably benign	Het
Nup50	A	G	15: 84,823,993 (GRCm39)	T449A	possibly damaging	Het
Nup98	A	G	7: 101,784,087 (GRCm39)	S1082P	possibly damaging	Het
Or8b1b	C	A	9: 38,375,815 (GRCm39)	H159Q	probably benign	Het
Otub1	T	C	19: 7,176,571 (GRCm39)	I188V	probably benign	Het
Pcdhac2	T	C	18: 37,279,186 (GRCm39)	I722T	possibly damaging	Het
Pcsk7	T	A	9: 45,825,646 (GRCm39)	D292E	probably damaging	Het
Peli2	T	A	14: 48,490,174 (GRCm39)	D215E	probably benign	Het
Ppp1r9a	T	C	6: 5,156,242 (GRCm39)		probably null	Het
Ppp2r1b	A	G	9: 50,773,725 (GRCm39)	K136R	possibly damaging	Het
Prpf3	T	C	3: 95,755,115 (GRCm39)	K157E	probably damaging	Het
Prss50	T	C	9: 110,690,336 (GRCm39)	S160P	probably damaging	Het
Ptprb	T	C	10: 116,216,774 (GRCm39)	V2251A	probably damaging	Het
Rgs6	G	A	12: 83,162,951 (GRCm39)	E386K	probably damaging	Het
Rida	A	G	15: 34,495,250 (GRCm39)	I5T	probably benign	Het
Rpe	A	G	1: 66,740,169 (GRCm39)	H35R	probably damaging	Het
Sema4b	T	A	7: 79,868,771 (GRCm39)	D321E	probably benign	Het
Slc22a13	G	A	9: 119,038,113 (GRCm39)	A5V	probably benign	Het
Snta1	C	T	2: 154,218,926 (GRCm39)		probably null	Het
Spdye4c	T	A	2: 128,437,632 (GRCm39)	N220K	probably benign	Het
Sult1c2	G	T	17: 54,269,176 (GRCm39)	A280E	possibly damaging	Het
Tfr2	A	G	5: 137,581,561 (GRCm39)	E579G	probably benign	Het
Tmem221	A	G	8: 72,011,182 (GRCm39)	L91P	probably damaging	Het
Tspear	T	A	10: 77,706,253 (GRCm39)	L341H	possibly damaging	Het
Vmn1r17	A	G	6: 57,338,317 (GRCm39)	V16A	probably benign	Het
Vmn1r188	A	G	13: 22,272,603 (GRCm39)	R186G	probably damaging	Het
Wfikkn1	A	G	17: 26,097,565 (GRCm39)	V253A	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
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'- AGCCTGCTCCCGTGAAG -3'
(R):5'- TAGTATCAGTGGCCTCCACG -3'

Posted On

2014-04-13