Incidental Mutation 'R4530:Xndc1'
| ID |
377837 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Xndc1
|
| Ensembl Gene |
ENSMUSG00000099481 |
| Gene Name |
Xrcc1 N-terminal domain containing 1 |
| Synonyms |
Xndr |
| MMRRC Submission |
041770-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R4530 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
7 |
| Chromosomal Location |
101714718-101732972 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 101727942 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Lysine
at position 85
(N85K)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000122430
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000084843]
[ENSMUST00000094129]
[ENSMUST00000094130]
[ENSMUST00000106950]
[ENSMUST00000123372]
[ENSMUST00000124189]
[ENSMUST00000139104]
[ENSMUST00000142629]
[ENSMUST00000146450]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000084843
AA Change: N175K
PolyPhen 2
Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000081903
Gene: ENSMUSG00000070425
AA Change: N175K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:XRCC1_N
|
1 |
150 |
1.4e-54 |
PFAM |
|
low complexity region
|
254 |
267 |
N/A |
INTRINSIC |
|
low complexity region
|
275 |
280 |
N/A |
INTRINSIC |
|
low complexity region
|
297 |
311 |
N/A |
INTRINSIC |
|
low complexity region
|
345 |
362 |
N/A |
INTRINSIC |
|
low complexity region
|
403 |
415 |
N/A |
INTRINSIC |
|
low complexity region
|
416 |
428 |
N/A |
INTRINSIC |
|
ANK
|
439 |
469 |
1.58e3 |
SMART |
|
low complexity region
|
484 |
496 |
N/A |
INTRINSIC |
|
ANK
|
522 |
551 |
1.74e0 |
SMART |
|
Pfam:TRP_2
|
557 |
619 |
1e-24 |
PFAM |
|
Pfam:Ion_trans
|
716 |
1024 |
1.7e-24 |
PFAM |
|
Pfam:PKD_channel
|
774 |
1019 |
2.4e-12 |
PFAM |
|
low complexity region
|
1070 |
1081 |
N/A |
INTRINSIC |
|
low complexity region
|
1093 |
1104 |
N/A |
INTRINSIC |
|
coiled coil region
|
1122 |
1162 |
N/A |
INTRINSIC |
|
low complexity region
|
1220 |
1236 |
N/A |
INTRINSIC |
|
low complexity region
|
1247 |
1263 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000094129
AA Change: N175K
PolyPhen 2
Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000091679
Gene: ENSMUSG00000070425
AA Change: N175K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:XRCC1_N
|
1 |
152 |
1.2e-27 |
PFAM |
|
low complexity region
|
254 |
267 |
N/A |
INTRINSIC |
|
low complexity region
|
275 |
280 |
N/A |
INTRINSIC |
|
low complexity region
|
297 |
311 |
N/A |
INTRINSIC |
|
low complexity region
|
345 |
362 |
N/A |
INTRINSIC |
|
low complexity region
|
403 |
415 |
N/A |
INTRINSIC |
|
low complexity region
|
416 |
428 |
N/A |
INTRINSIC |
|
ANK
|
439 |
469 |
1.58e3 |
SMART |
|
low complexity region
|
484 |
496 |
N/A |
INTRINSIC |
|
ANK
|
522 |
551 |
1.74e0 |
SMART |
|
Pfam:TRP_2
|
557 |
619 |
2.8e-28 |
PFAM |
|
transmembrane domain
|
719 |
741 |
N/A |
INTRINSIC |
|
Pfam:PKD_channel
|
772 |
1019 |
3.8e-12 |
PFAM |
|
Pfam:Ion_trans
|
796 |
1012 |
3.9e-31 |
PFAM |
|
low complexity region
|
1070 |
1081 |
N/A |
INTRINSIC |
|
low complexity region
|
1093 |
1104 |
N/A |
INTRINSIC |
|
coiled coil region
|
1122 |
1162 |
N/A |
INTRINSIC |
|
low complexity region
|
1220 |
1236 |
N/A |
INTRINSIC |
|
low complexity region
|
1247 |
1263 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000094130
AA Change: N175K
PolyPhen 2
Score 0.070 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000091680
Gene: ENSMUSG00000099481
AA Change: N175K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:XRCC1_N
|
1 |
152 |
5.2e-29 |
PFAM |
|
low complexity region
|
254 |
267 |
N/A |
INTRINSIC |
|
low complexity region
|
275 |
280 |
N/A |
INTRINSIC |
|
low complexity region
|
297 |
311 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
324 |
345 |
2.69e-6 |
PROSPERO |
|
low complexity region
|
346 |
379 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
380 |
401 |
2.69e-6 |
PROSPERO |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000106950
AA Change: N175K
PolyPhen 2
Score 0.070 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000102563
Gene: ENSMUSG00000099481
AA Change: N175K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:XRCC1_N
|
1 |
152 |
5.2e-29 |
PFAM |
|
low complexity region
|
254 |
267 |
N/A |
INTRINSIC |
|
low complexity region
|
275 |
280 |
N/A |
INTRINSIC |
|
low complexity region
|
297 |
311 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
324 |
345 |
2.69e-6 |
PROSPERO |
|
low complexity region
|
346 |
379 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
380 |
401 |
2.69e-6 |
PROSPERO |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000123372
AA Change: N175K
PolyPhen 2
Score 0.070 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000121068
Gene: ENSMUSG00000070425
AA Change: N175K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:XRCC1_N
|
1 |
152 |
5.2e-29 |
PFAM |
|
low complexity region
|
254 |
267 |
N/A |
INTRINSIC |
|
low complexity region
|
275 |
280 |
N/A |
INTRINSIC |
|
low complexity region
|
297 |
311 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
324 |
345 |
2.69e-6 |
PROSPERO |
|
low complexity region
|
346 |
379 |
N/A |
INTRINSIC |
|
internal_repeat_1
|
380 |
401 |
2.69e-6 |
PROSPERO |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000124189
|
| SMART Domains |
Protein: ENSMUSP00000116934
Gene: ENSMUSG00000100254
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
29 |
41 |
N/A |
INTRINSIC |
|
low complexity region
|
42 |
54 |
N/A |
INTRINSIC |
|
ANK
|
65 |
95 |
1.58e3 |
SMART |
|
low complexity region
|
110 |
122 |
N/A |
INTRINSIC |
|
ANK
|
148 |
177 |
1.74e0 |
SMART |
|
Pfam:TRP_2
|
183 |
245 |
9.1e-29 |
PFAM |
|
transmembrane domain
|
345 |
367 |
N/A |
INTRINSIC |
|
Pfam:PKD_channel
|
398 |
645 |
1.4e-12 |
PFAM |
|
Pfam:Ion_trans
|
422 |
638 |
1e-31 |
PFAM |
|
low complexity region
|
696 |
707 |
N/A |
INTRINSIC |
|
low complexity region
|
719 |
730 |
N/A |
INTRINSIC |
|
coiled coil region
|
748 |
788 |
N/A |
INTRINSIC |
|
low complexity region
|
846 |
862 |
N/A |
INTRINSIC |
|
low complexity region
|
873 |
889 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000125197
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000139104
AA Change: N85K
PolyPhen 2
Score 0.210 (Sensitivity: 0.92; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000122430
Gene: ENSMUSG00000070425
AA Change: N85K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:XRCC1_N
|
1 |
62 |
3.5e-14 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000153176
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000155078
AA Change: N86K
|
| SMART Domains |
Protein: ENSMUSP00000123466
Gene: ENSMUSG00000070425
AA Change: N86K
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:XRCC1_N
|
1 |
62 |
4.4e-22 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000140395
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000143839
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000142629
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000146450
|
| SMART Domains |
Protein: ENSMUSP00000117300
Gene: ENSMUSG00000099481
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:XRCC1_N
|
1 |
152 |
1.1e-29 |
PFAM |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.6%
|
| Validation Efficiency |
93% (37/40) |
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 36 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adcy4 |
T |
C |
14: 56,016,485 (GRCm39) |
D322G |
probably damaging |
Het |
| Akap9 |
T |
A |
5: 4,093,948 (GRCm39) |
F2157I |
probably damaging |
Het |
| Arhgap42 |
T |
C |
9: 9,011,433 (GRCm39) |
D451G |
probably damaging |
Het |
| Arhgef7 |
T |
C |
8: 11,850,802 (GRCm39) |
M144T |
possibly damaging |
Het |
| Arid4b |
C |
A |
13: 14,301,040 (GRCm39) |
T41N |
probably damaging |
Het |
| Axin1 |
T |
A |
17: 26,407,146 (GRCm39) |
Y580N |
probably benign |
Het |
| Cdc27 |
T |
C |
11: 104,419,252 (GRCm39) |
N227D |
possibly damaging |
Het |
| Cetn4 |
C |
T |
3: 37,364,094 (GRCm39) |
V39I |
probably benign |
Het |
| Clec2h |
A |
G |
6: 128,639,457 (GRCm39) |
D18G |
possibly damaging |
Het |
| Clec4e |
T |
C |
6: 123,266,733 (GRCm39) |
|
probably benign |
Het |
| Cntnap4 |
T |
C |
8: 113,584,842 (GRCm39) |
I1093T |
probably benign |
Het |
| Dner |
G |
T |
1: 84,560,736 (GRCm39) |
N136K |
probably damaging |
Het |
| Gpr158 |
A |
G |
2: 21,373,811 (GRCm39) |
S249G |
probably benign |
Het |
| Il16 |
A |
C |
7: 83,330,518 (GRCm39) |
|
probably benign |
Het |
| Intu |
T |
G |
3: 40,637,794 (GRCm39) |
C427G |
possibly damaging |
Het |
| Kif21a |
A |
C |
15: 90,852,292 (GRCm39) |
|
probably null |
Het |
| Lin54 |
G |
A |
5: 100,594,419 (GRCm39) |
T582I |
possibly damaging |
Het |
| Mroh7 |
T |
C |
4: 106,577,634 (GRCm39) |
E348G |
possibly damaging |
Het |
| Or10g6 |
G |
A |
9: 39,934,589 (GRCm39) |
R300K |
probably benign |
Het |
| Or2h1b |
C |
T |
17: 37,462,498 (GRCm39) |
V122M |
possibly damaging |
Het |
| Or8g2b |
G |
T |
9: 39,751,379 (GRCm39) |
M216I |
probably benign |
Het |
| Or8k38 |
T |
C |
2: 86,487,905 (GRCm39) |
D299G |
probably benign |
Het |
| Pabir3 |
G |
A |
X: 52,382,376 (GRCm39) |
R94H |
possibly damaging |
Het |
| Plbd1 |
T |
A |
6: 136,628,823 (GRCm39) |
I82F |
probably benign |
Het |
| Prss43 |
A |
T |
9: 110,658,572 (GRCm39) |
M291L |
probably benign |
Het |
| Rap1gds1 |
T |
C |
3: 138,663,186 (GRCm39) |
N338D |
probably damaging |
Het |
| Rsf1 |
CGGCGGCGG |
CGGCGGCGGGGGCGGCGG |
7: 97,229,130 (GRCm39) |
|
probably benign |
Het |
| Stip1 |
G |
T |
19: 7,013,026 (GRCm39) |
N19K |
probably benign |
Het |
| Tat |
T |
A |
8: 110,722,842 (GRCm39) |
F301L |
probably benign |
Het |
| Tmprss11a |
C |
A |
5: 86,576,540 (GRCm39) |
V104L |
possibly damaging |
Het |
| Ttc3 |
T |
A |
16: 94,267,736 (GRCm39) |
|
probably benign |
Het |
| Tubgcp3 |
G |
T |
8: 12,713,932 (GRCm39) |
L62I |
probably damaging |
Het |
| Vcan |
A |
T |
13: 89,852,147 (GRCm39) |
F938I |
probably damaging |
Het |
| Wrap73 |
A |
G |
4: 154,241,164 (GRCm39) |
|
probably benign |
Het |
| Zfp282 |
C |
T |
6: 47,867,567 (GRCm39) |
P248S |
probably benign |
Het |
| Zfp930 |
C |
T |
8: 69,681,483 (GRCm39) |
Q393* |
probably null |
Het |
|
| Other mutations in Xndc1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
R0415:Xndc1
|
UTSW |
7 |
101,729,823 (GRCm39) |
splice site |
probably benign |
|
|
R0648:Xndc1
|
UTSW |
7 |
101,728,031 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R1990:Xndc1
|
UTSW |
7 |
101,722,398 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1991:Xndc1
|
UTSW |
7 |
101,722,398 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4290:Xndc1
|
UTSW |
7 |
101,730,694 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R4295:Xndc1
|
UTSW |
7 |
101,730,694 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R4815:Xndc1
|
UTSW |
7 |
101,722,523 (GRCm39) |
missense |
probably null |
1.00 |
|
R5384:Xndc1
|
UTSW |
7 |
101,731,395 (GRCm39) |
missense |
probably benign |
0.12 |
|
R6838:Xndc1
|
UTSW |
7 |
101,722,476 (GRCm39) |
missense |
possibly damaging |
0.79 |
|
R6940:Xndc1
|
UTSW |
7 |
101,727,094 (GRCm39) |
missense |
probably benign |
0.15 |
|
R7310:Xndc1
|
UTSW |
7 |
101,727,938 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R7375:Xndc1
|
UTSW |
7 |
101,730,687 (GRCm39) |
splice site |
probably null |
|
|
R8271:Xndc1
|
UTSW |
7 |
101,728,343 (GRCm39) |
missense |
possibly damaging |
0.58 |
|
R8802:Xndc1
|
UTSW |
7 |
101,720,539 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
R8876:Xndc1
|
UTSW |
7 |
101,729,754 (GRCm39) |
missense |
probably benign |
0.06 |
|
R8996:Xndc1
|
UTSW |
7 |
101,722,518 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9230:Xndc1
|
UTSW |
7 |
101,722,476 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9716:Xndc1
|
UTSW |
7 |
101,725,114 (GRCm39) |
missense |
probably damaging |
1.00 |
|
X0060:Xndc1
|
UTSW |
7 |
101,728,355 (GRCm39) |
missense |
probably benign |
0.08 |
|
X0065:Xndc1
|
UTSW |
7 |
101,730,692 (GRCm39) |
missense |
probably benign |
0.03 |
|
| Predicted Primers |
PCR Primer
(F):5'- GCCAGTGCCAGGTGGAATAATG -3'
(R):5'- TAGACCTTAAGTGACTAACCAGGG -3'
Sequencing Primer
(F):5'- ACTTTGTAGACCAGGCTGAC -3'
(R):5'- GTACATACGTCTGGGGAT -3'
|
| Posted On |
2016-04-11 |
Incidental Mutation