Incidental Mutation 'R1614:Smarcd3'
| ID |
176990 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smarcd3
|
| Ensembl Gene |
ENSMUSG00000028949 |
| Gene Name |
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 |
| Synonyms |
2210409C08Rik, BAF60C, 1500001J14Rik |
| MMRRC Submission |
039651-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R1614 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
24797620-24829649 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 24799874 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Proline
at position 299
(S299P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000030791
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030791]
[ENSMUST00000088295]
[ENSMUST00000121863]
[ENSMUST00000195943]
[ENSMUST00000197318]
|
| AlphaFold |
Q6P9Z1 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000030791
AA Change: S299P
PolyPhen 2
Score 0.932 (Sensitivity: 0.80; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000030791
Gene: ENSMUSG00000028949
AA Change: S299P
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
40 |
55 |
N/A |
INTRINSIC |
|
low complexity region
|
72 |
89 |
N/A |
INTRINSIC |
|
low complexity region
|
93 |
102 |
N/A |
INTRINSIC |
|
Blast:KISc
|
103 |
239 |
5e-41 |
BLAST |
|
SWIB
|
259 |
338 |
3.6e-29 |
SMART |
|
Blast:MYSc
|
420 |
466 |
1e-11 |
BLAST |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000088295
|
| SMART Domains |
Protein: ENSMUSP00000085633
Gene: ENSMUSG00000038181
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
19 |
N/A |
INTRINSIC |
|
Pfam:Fringe
|
143 |
298 |
3.2e-11 |
PFAM |
|
Pfam:CHGN
|
242 |
755 |
1.7e-144 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000102432
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000121863
|
| SMART Domains |
Protein: ENSMUSP00000112804
Gene: ENSMUSG00000038181
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
19 |
N/A |
INTRINSIC |
|
Pfam:Fringe
|
143 |
298 |
3.2e-11 |
PFAM |
|
Pfam:CHGN
|
242 |
755 |
3e-176 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000140744
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000143501
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144518
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000195943
AA Change: S270P
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000143437
Gene: ENSMUSG00000028949
AA Change: S270P
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
11 |
26 |
N/A |
INTRINSIC |
|
low complexity region
|
43 |
60 |
N/A |
INTRINSIC |
|
low complexity region
|
64 |
73 |
N/A |
INTRINSIC |
|
Blast:KISc
|
74 |
210 |
2e-41 |
BLAST |
|
SWIB
|
230 |
309 |
2.3e-31 |
SMART |
|
Blast:MYSc
|
391 |
437 |
8e-12 |
BLAST |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000147857
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000145565
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000144995
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000197933
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000197318
|
| SMART Domains |
Protein: ENSMUSP00000143185
Gene: ENSMUSG00000038181
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:CHGN
|
1 |
74 |
7.5e-22 |
PFAM |
|
| Meta Mutation Damage Score |
0.0928 |
| Coding Region Coverage |
- 1x: 99.0%
- 3x: 98.1%
- 10x: 95.4%
- 20x: 89.4%
|
| Validation Efficiency |
100% (53/53) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the SWI/SNF family of proteins, whose members display helicase and ATPase activities and which are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI and has sequence similarity to the yeast Swp73 protein. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 46 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Arl9 |
A |
G |
5: 77,158,412 (GRCm39) |
T165A |
probably benign |
Het |
| Atpaf1 |
A |
T |
4: 115,653,954 (GRCm39) |
K201N |
possibly damaging |
Het |
| Cacna1b |
G |
T |
2: 24,580,819 (GRCm39) |
Q676K |
possibly damaging |
Het |
| Ccdc88c |
A |
T |
12: 100,879,243 (GRCm39) |
H1959Q |
probably benign |
Het |
| Cep162 |
T |
C |
9: 87,094,985 (GRCm39) |
D808G |
probably damaging |
Het |
| Chct1 |
T |
G |
11: 85,063,690 (GRCm39) |
S28A |
possibly damaging |
Het |
| Chtf18 |
A |
G |
17: 25,946,064 (GRCm39) |
L42P |
probably benign |
Het |
| Cox7c |
A |
G |
13: 86,193,904 (GRCm39) |
F40L |
probably benign |
Het |
| Dock7 |
C |
T |
4: 98,949,517 (GRCm39) |
V442I |
probably benign |
Het |
| Dst |
T |
C |
1: 34,314,344 (GRCm39) |
F4198S |
probably damaging |
Het |
| Fam13a |
T |
A |
6: 58,917,169 (GRCm39) |
D569V |
probably damaging |
Het |
| Gm6741 |
T |
A |
17: 91,544,424 (GRCm39) |
H62Q |
probably benign |
Het |
| Gnptab |
A |
G |
10: 88,250,451 (GRCm39) |
T172A |
probably benign |
Het |
| Greb1 |
A |
G |
12: 16,751,172 (GRCm39) |
S1013P |
probably damaging |
Het |
| Insl5 |
A |
T |
4: 102,883,846 (GRCm39) |
L25* |
probably null |
Het |
| Ipo13 |
A |
G |
4: 117,761,815 (GRCm39) |
S462P |
probably benign |
Het |
| Itgb1 |
G |
A |
8: 129,446,546 (GRCm39) |
C401Y |
probably damaging |
Het |
| Kcnh7 |
G |
T |
2: 62,680,948 (GRCm39) |
A213E |
probably benign |
Het |
| Kcnv1 |
G |
A |
15: 44,977,840 (GRCm39) |
T66M |
probably damaging |
Het |
| Mesp2 |
T |
C |
7: 79,461,367 (GRCm39) |
S231P |
probably benign |
Het |
| Nabp1 |
T |
C |
1: 51,510,511 (GRCm39) |
N164D |
possibly damaging |
Het |
| Nop53 |
A |
G |
7: 15,679,890 (GRCm39) |
V30A |
probably benign |
Het |
| Or1j17 |
T |
G |
2: 36,578,321 (GRCm39) |
Y102* |
probably null |
Het |
| Or4a73 |
T |
A |
2: 89,421,040 (GRCm39) |
I140L |
possibly damaging |
Het |
| Or4f54 |
T |
A |
2: 111,123,411 (GRCm39) |
V266E |
probably damaging |
Het |
| Or4f62 |
T |
A |
2: 111,986,862 (GRCm39) |
C189S |
probably damaging |
Het |
| Pcsk5 |
G |
A |
19: 17,492,620 (GRCm39) |
R918C |
probably damaging |
Het |
| Pecam1 |
T |
C |
11: 106,571,905 (GRCm39) |
D554G |
probably benign |
Het |
| Polr2a |
T |
C |
11: 69,634,199 (GRCm39) |
I744V |
possibly damaging |
Het |
| Pop1 |
C |
A |
15: 34,530,356 (GRCm39) |
A918D |
possibly damaging |
Het |
| Ppp2r5e |
C |
G |
12: 75,516,341 (GRCm39) |
A239P |
probably damaging |
Het |
| Prmt3 |
A |
T |
7: 49,476,467 (GRCm39) |
I359F |
possibly damaging |
Het |
| Proz |
G |
A |
8: 13,116,904 (GRCm39) |
C152Y |
probably damaging |
Het |
| Ptgfr |
A |
C |
3: 151,507,416 (GRCm39) |
Y316D |
probably benign |
Het |
| Ralgapa2 |
G |
T |
2: 146,230,532 (GRCm39) |
S1011Y |
probably damaging |
Het |
| Rnf43 |
C |
T |
11: 87,622,485 (GRCm39) |
R529* |
probably null |
Het |
| Slc17a6 |
G |
A |
7: 51,296,025 (GRCm39) |
|
probably benign |
Het |
| Slc25a19 |
A |
T |
11: 115,507,449 (GRCm39) |
C224* |
probably null |
Het |
| Stard9 |
T |
C |
2: 120,528,156 (GRCm39) |
F1471S |
possibly damaging |
Het |
| Strada |
A |
C |
11: 106,059,145 (GRCm39) |
V211G |
probably damaging |
Het |
| Tom1l1 |
T |
C |
11: 90,574,080 (GRCm39) |
E68G |
probably damaging |
Het |
| Vmn2r27 |
T |
G |
6: 124,200,893 (GRCm39) |
I355L |
probably benign |
Het |
| Vmn2r68 |
A |
T |
7: 84,870,946 (GRCm39) |
M779K |
possibly damaging |
Het |
| Zbtb18 |
T |
C |
1: 177,274,736 (GRCm39) |
L23P |
probably damaging |
Het |
| Zfp112 |
G |
T |
7: 23,826,024 (GRCm39) |
C664F |
probably damaging |
Het |
| Zfp955a |
A |
T |
17: 33,461,306 (GRCm39) |
N275K |
possibly damaging |
Het |
|
| Other mutations in Smarcd3 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL02401:Smarcd3
|
APN |
5 |
24,798,717 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0135:Smarcd3
|
UTSW |
5 |
24,800,497 (GRCm39) |
unclassified |
probably benign |
|
|
R1617:Smarcd3
|
UTSW |
5 |
24,800,192 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1753:Smarcd3
|
UTSW |
5 |
24,800,820 (GRCm39) |
nonsense |
probably null |
|
|
R1879:Smarcd3
|
UTSW |
5 |
24,798,019 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2307:Smarcd3
|
UTSW |
5 |
24,800,746 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3800:Smarcd3
|
UTSW |
5 |
24,798,225 (GRCm39) |
nonsense |
probably null |
|
|
R4592:Smarcd3
|
UTSW |
5 |
24,797,802 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6369:Smarcd3
|
UTSW |
5 |
24,799,982 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6388:Smarcd3
|
UTSW |
5 |
24,801,024 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R7077:Smarcd3
|
UTSW |
5 |
24,799,960 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7078:Smarcd3
|
UTSW |
5 |
24,798,067 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R7341:Smarcd3
|
UTSW |
5 |
24,800,435 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R7426:Smarcd3
|
UTSW |
5 |
24,800,810 (GRCm39) |
missense |
probably benign |
0.30 |
|
R7806:Smarcd3
|
UTSW |
5 |
24,798,260 (GRCm39) |
missense |
probably benign |
0.45 |
|
R7935:Smarcd3
|
UTSW |
5 |
24,801,024 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8685:Smarcd3
|
UTSW |
5 |
24,800,988 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8769:Smarcd3
|
UTSW |
5 |
24,803,792 (GRCm39) |
missense |
probably benign |
|
|
R8877:Smarcd3
|
UTSW |
5 |
24,798,990 (GRCm39) |
missense |
possibly damaging |
0.93 |
|
R8984:Smarcd3
|
UTSW |
5 |
24,798,986 (GRCm39) |
missense |
probably null |
0.99 |
|
R9240:Smarcd3
|
UTSW |
5 |
24,801,831 (GRCm39) |
missense |
probably benign |
0.21 |
|
RF007:Smarcd3
|
UTSW |
5 |
24,801,068 (GRCm39) |
missense |
probably damaging |
0.98 |
|
| Predicted Primers |
PCR Primer
(F):5'- AGGAGATTCCATCACCAGATGCCC -3'
(R):5'- ATACTGCTAAGGACCCTAACCTCCG -3'
Sequencing Primer
(F):5'- AGATGCCCTCCGTACCAGTAG -3'
(R):5'- TAACCTCCGTGCCCCTG -3'
|
| Posted On |
2014-04-24 |
Incidental Mutation