Incidental Mutation 'R4224:Khdc3'
| ID |
319966 |
| 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 |
041044-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.094)
|
| Stock # |
R4224 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
9 |
| Chromosomal Location |
73009118-73011720 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to G
at 73010153 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Histidine to Aspartic acid
at position 70
(H70D)
|
| 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: H70D
PolyPhen 2
Score 0.920 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000034737
Gene: ENSMUSG00000092622
AA Change: H70D
| 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: H70D
PolyPhen 2
Score 0.920 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000132527
Gene: ENSMUSG00000092622
AA Change: H70D
| 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 |
possibly damaging
Transcript: ENSMUST00000172578
AA Change: H70D
PolyPhen 2
Score 0.711 (Sensitivity: 0.86; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000133850
Gene: ENSMUSG00000092622
AA Change: H70D
| Domain | Start | End | E-Value | Type |
|---|
|
PDB:3V69|B
|
1 |
75 |
4e-49 |
PDB |
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000173734
AA Change: H70D
PolyPhen 2
Score 0.920 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000133915
Gene: ENSMUSG00000092622
AA Change: H70D
| 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: H70D
|
| SMART Domains |
Protein: ENSMUSP00000134473
Gene: ENSMUSG00000092310
AA Change: H70D
| 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: 99.3%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 96.0%
|
| Validation Efficiency |
95% (42/44) |
| 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: 38 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 9330182O14Rik |
T |
C |
15: 40,005,672 (GRCm39) |
|
probably null |
Het |
| Abl2 |
A |
G |
1: 156,461,417 (GRCm39) |
T440A |
probably damaging |
Het |
| Acat2 |
T |
C |
17: 13,181,772 (GRCm39) |
|
probably benign |
Het |
| Acsbg1 |
C |
T |
9: 54,523,325 (GRCm39) |
R434H |
possibly damaging |
Het |
| Aif1l |
A |
T |
2: 31,852,251 (GRCm39) |
S40C |
probably damaging |
Het |
| Atosa |
T |
A |
9: 74,916,008 (GRCm39) |
N209K |
probably damaging |
Het |
| Atp6v1a |
C |
A |
16: 43,922,174 (GRCm39) |
A355S |
probably damaging |
Het |
| Corin |
T |
C |
5: 72,500,451 (GRCm39) |
E391G |
probably damaging |
Het |
| Dnah11 |
T |
G |
12: 118,094,627 (GRCm39) |
S814R |
probably benign |
Het |
| Fer1l4 |
A |
C |
2: 155,862,309 (GRCm39) |
V1788G |
probably benign |
Het |
| Gm7964 |
T |
G |
7: 83,406,030 (GRCm39) |
N281K |
probably damaging |
Het |
| Grin1 |
T |
C |
2: 25,187,332 (GRCm39) |
|
probably benign |
Het |
| Ica1 |
T |
C |
6: 8,659,960 (GRCm39) |
K112R |
probably benign |
Het |
| Itpr3 |
T |
C |
17: 27,326,232 (GRCm39) |
V1334A |
probably damaging |
Het |
| Lama3 |
T |
C |
18: 12,583,460 (GRCm39) |
C683R |
probably damaging |
Het |
| Mettl21a |
G |
T |
1: 64,647,115 (GRCm39) |
Y147* |
probably null |
Het |
| Mr1 |
A |
T |
1: 155,006,465 (GRCm39) |
I294N |
possibly damaging |
Het |
| Or52z12 |
A |
G |
7: 103,233,966 (GRCm39) |
T246A |
probably damaging |
Het |
| Or7e170 |
T |
A |
9: 19,794,896 (GRCm39) |
Y235F |
probably benign |
Het |
| Pals1 |
A |
G |
12: 78,876,492 (GRCm39) |
K479E |
probably damaging |
Het |
| Pcdhgb7 |
T |
A |
18: 37,886,856 (GRCm39) |
D675E |
probably benign |
Het |
| Polr1has |
T |
C |
17: 37,269,617 (GRCm39) |
|
probably benign |
Het |
| Ptbp1 |
T |
C |
10: 79,695,047 (GRCm39) |
I125T |
probably benign |
Het |
| Rnf213 |
C |
T |
11: 119,327,649 (GRCm39) |
R1879* |
probably null |
Het |
| Slc8a1 |
A |
G |
17: 81,956,781 (GRCm39) |
F86L |
probably damaging |
Het |
| Spdya |
G |
A |
17: 71,869,519 (GRCm39) |
V105I |
probably benign |
Het |
| Sspo |
G |
T |
6: 48,428,091 (GRCm39) |
V313L |
possibly damaging |
Het |
| Stard9 |
A |
G |
2: 120,495,472 (GRCm39) |
T116A |
possibly damaging |
Het |
| Tnnt1 |
T |
C |
7: 4,513,006 (GRCm39) |
H92R |
probably damaging |
Het |
| Trim37 |
T |
A |
11: 87,107,289 (GRCm39) |
C907S |
probably damaging |
Het |
| Trim43b |
T |
A |
9: 88,972,692 (GRCm39) |
Q154L |
probably benign |
Het |
| Tssk3 |
T |
C |
4: 129,384,392 (GRCm39) |
D3G |
probably benign |
Het |
| Ubash3a |
T |
C |
17: 31,456,902 (GRCm39) |
Y521H |
probably damaging |
Het |
| Vmn1r73 |
T |
C |
7: 11,490,506 (GRCm39) |
I108T |
probably damaging |
Het |
| Vmn2r14 |
A |
G |
5: 109,364,149 (GRCm39) |
M589T |
probably benign |
Het |
| Vmn2r60 |
A |
T |
7: 41,765,952 (GRCm39) |
T20S |
probably benign |
Het |
| Vps13b |
A |
G |
15: 35,876,565 (GRCm39) |
T2799A |
probably damaging |
Het |
| Zcchc18 |
A |
T |
X: 135,895,415 (GRCm39) |
N10I |
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 |
|
|
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'- CGGCTACTGGAAATCATGTTTGG -3'
(R):5'- AAGACTTGCTGGACAGGATAGC -3'
Sequencing Primer
(F):5'- GAAAGGCCAAGGTAACCTTTTCCTG -3'
(R):5'- TTGCTGGACAGGATAGCCCTAC -3'
|
| Posted On |
2015-06-12 |
Incidental Mutation