Mutagenetix > Incidental Mutation

Incidental Mutation 'R8362:Khdc3'

646001

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

067808-MU

Accession Numbers

Essential gene?

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

Stock #

R8362 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

73009118-73011720 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 73010848 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Tyrosine at position 233 (N233Y)

Ref Sequence

ENSEMBL: ENSMUSP00000034737 (fasta)

Gene Model

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

AlphaFold

Q9CWU5

PDB Structure

Filia-N crystal structure [X-RAY DIFFRACTION]

Predicted Effect

possibly damaging
Transcript: ENSMUST00000034737
AA Change: N233Y

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000034737
Gene: ENSMUSG00000092622
AA Change: N233Y

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 damaging
Transcript: ENSMUST00000167514
AA Change: N209Y

PolyPhen 2 Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000132527
Gene: ENSMUSG00000092622
AA Change: N209Y

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 damaging
Transcript: ENSMUST00000173734
AA Change: N233Y

PolyPhen 2 Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000133915
Gene: ENSMUSG00000092622
AA Change: N233Y

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: N143Y

SMART Domains

Protein: ENSMUSP00000134473
Gene: ENSMUSG00000092310
AA Change: N143Y

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: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.2%

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: 52 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1810009A15Rik	T	A	19: 8,867,395 (GRCm39)	S65T	probably damaging	Het
Abcb1b	A	T	5: 8,848,758 (GRCm39)	N6I	probably benign	Het
Abr	A	T	11: 76,369,954 (GRCm39)	I145N	probably benign	Het
Alcam	A	T	16: 52,115,387 (GRCm39)	Y244N	probably damaging	Het
Amotl1	G	A	9: 14,556,218 (GRCm39)	A36V	probably benign	Het
Ankrd11	A	T	8: 123,618,797 (GRCm39)	L1685Q	probably damaging	Het
Ascc3	A	C	10: 50,518,692 (GRCm39)	Q332H	possibly damaging	Het
Cdc42bpa	C	T	1: 179,989,690 (GRCm39)	L1720F	probably damaging	Het
Clec4b1	T	C	6: 123,027,602 (GRCm39)	S20P	probably benign	Het
Cpt1a	C	T	19: 3,420,744 (GRCm39)	R401*	probably null	Het
Dnah12	T	A	14: 26,576,788 (GRCm39)	Y3013N	probably damaging	Het
Dop1a	G	A	9: 86,395,941 (GRCm39)	R801H	probably benign	Het
Flywch1	G	T	17: 23,975,682 (GRCm39)	T520N	probably damaging	Het
Fndc1	A	G	17: 8,001,207 (GRCm39)	S190P	unknown	Het
Gabra1	G	T	11: 42,066,831 (GRCm39)	Q28K	probably benign	Het
Gria2	T	C	3: 80,615,197 (GRCm39)	M428V	possibly damaging	Het
H13	T	A	2: 152,528,311 (GRCm39)	I220N	unknown	Het
Hars2	T	A	18: 36,923,228 (GRCm39)	F412L	probably benign	Het
Hecw2	A	T	1: 54,079,650 (GRCm39)	M1K	probably null	Het
Homer1	T	A	13: 93,502,797 (GRCm39)	S192T	unknown	Het
Itga2b	T	A	11: 102,352,189 (GRCm39)	D464V	probably damaging	Het
Ivd	T	A	2: 118,708,422 (GRCm39)	C379S	probably damaging	Het
Lrrc37	A	G	11: 103,506,163 (GRCm39)	V1935A	probably benign	Het
Lrrfip1	T	A	1: 90,981,423 (GRCm39)	L15Q	probably damaging	Het
Megf8	C	A	7: 25,039,943 (GRCm39)	P986Q	probably benign	Het
Morc2b	G	T	17: 33,357,295 (GRCm39)	T159K	possibly damaging	Het
Nudt5	A	G	2: 5,858,322 (GRCm39)		probably null	Het
Or6c211	G	T	10: 129,506,100 (GRCm39)	A96E	possibly damaging	Het
Paqr5	A	T	9: 61,879,945 (GRCm39)	Y116*	probably null	Het
Pcnx1	A	C	12: 82,013,830 (GRCm39)	S623R		Het
Polr1a	T	C	6: 71,941,651 (GRCm39)	V1053A	probably benign	Het
Ptprt	A	T	2: 161,393,667 (GRCm39)	D1252E	probably damaging	Het
Qser1	A	G	2: 104,620,246 (GRCm39)	S189P	probably damaging	Het
Rasal1	C	T	5: 120,813,485 (GRCm39)	R620W	probably damaging	Het
Rbms1	C	T	2: 60,793,083 (GRCm39)	M9I	probably benign	Het
Ska3	T	C	14: 58,054,105 (GRCm39)	N282D	probably benign	Het
Slc25a24	T	A	3: 109,065,878 (GRCm39)	I245N	possibly damaging	Het
Slc26a4	C	T	12: 31,594,506 (GRCm39)	V281I	probably benign	Het
Smg8	A	T	11: 86,968,881 (GRCm39)	Y958*	probably null	Het
Spata31	A	G	13: 65,070,044 (GRCm39)	T731A	possibly damaging	Het
Spg11	G	T	2: 121,948,842 (GRCm39)	A3D	unknown	Het
Srgap1	A	G	10: 121,691,383 (GRCm39)	Y284H	possibly damaging	Het
Stt3b	A	G	9: 115,083,988 (GRCm39)	I396T	probably damaging	Het
Tnxb	A	G	17: 34,931,946 (GRCm39)	T2160A	probably damaging	Het
Tprg1l	G	C	4: 154,244,815 (GRCm39)	T91S	possibly damaging	Het
Ush2a	G	A	1: 188,689,650 (GRCm39)	V5071I	probably damaging	Het
Vmn2r60	T	A	7: 41,844,954 (GRCm39)	N772K	probably damaging	Het
Vmn2r81	T	A	10: 79,103,283 (GRCm39)	W159R	probably benign	Het
Vmn2r93	G	A	17: 18,546,353 (GRCm39)	V742I	probably benign	Het
Zc3h13	C	A	14: 75,561,909 (GRCm39)	H654N	unknown	Het
Zfp516	T	C	18: 83,005,019 (GRCm39)	L641P	probably benign	Het
Zfp623	T	C	15: 75,819,488 (GRCm39)	V148A	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
R5261:Khdc3	UTSW	9	73,010,768 (GRCm39)	missense	possibly damaging	0.92
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'- CAACTCAGTAGAGGCTCTGG -3'
(R):5'- ACCTTCACAGGAGCCAACTG -3'

Sequencing Primer
(F):5'- TTCCGTGAAGGTCCCTGAGAC -3'
(R):5'- CGGACCTTCCCGGAAGC -3'

Posted On

2020-09-02