Incidental Mutation 'R5242:Smarcal1'
| ID |
400885 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Smarcal1
|
| Ensembl Gene |
ENSMUSG00000039354 |
| Gene Name |
SWI/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1 |
| Synonyms |
Mharp, 6030401P21Rik |
| MMRRC Submission |
042813-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R5242 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
1 |
| Chromosomal Location |
72622410-72672293 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 72630242 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Proline
at position 99
(S99P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000114848
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000047615]
[ENSMUST00000133123]
[ENSMUST00000152225]
|
| AlphaFold |
Q8BJL0 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000047615
AA Change: S261P
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000047589
Gene: ENSMUSG00000039354
AA Change: S261P
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
31 |
51 |
N/A |
INTRINSIC |
|
Pfam:HARP
|
214 |
268 |
3.6e-26 |
PFAM |
|
Pfam:HARP
|
302 |
356 |
1.2e-26 |
PFAM |
|
DEXDc
|
391 |
564 |
7.01e-17 |
SMART |
|
low complexity region
|
632 |
641 |
N/A |
INTRINSIC |
|
HELICc
|
697 |
780 |
8.17e-18 |
SMART |
|
low complexity region
|
879 |
889 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000133123
AA Change: S99P
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
| SMART Domains |
Protein: ENSMUSP00000114848
Gene: ENSMUSG00000039354
AA Change: S99P
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
31 |
51 |
N/A |
INTRINSIC |
|
Pfam:HARP
|
66 |
106 |
1.7e-14 |
PFAM |
|
Pfam:HARP
|
140 |
194 |
2.2e-28 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000136498
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000150725
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000152225
AA Change: S261P
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000137833
Gene: ENSMUSG00000039354
AA Change: S261P
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
31 |
51 |
N/A |
INTRINSIC |
|
Pfam:HARP
|
214 |
268 |
8e-29 |
PFAM |
|
Pfam:HARP
|
302 |
356 |
3e-26 |
PFAM |
|
DEXDc
|
391 |
564 |
7.01e-17 |
SMART |
|
low complexity region
|
632 |
641 |
N/A |
INTRINSIC |
|
HELICc
|
697 |
780 |
8.17e-18 |
SMART |
|
low complexity region
|
879 |
889 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000152814
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000156797
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 94.2%
|
| 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 is a member of the SWI/SNF family of proteins. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein shows sequence similarity to the E. coli RNA polymerase-binding protein HepA. Mutations in this gene are a cause of Schimke immunoosseous dysplasia (SIOD), an autosomal recessive disorder with the diagnostic features of spondyloepiphyseal dysplasia, renal dysfunction, and T-cell immunodeficiency. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele display reduced B cell counts and increased susceptibility to heat induced mortality. Treatment of homozygous null mice with alpha-amanitin results in phenotypes similar to Schimke Type Immunoosseous Dysplasia. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adgrl1 |
T |
C |
8: 84,657,711 (GRCm39) |
V439A |
possibly damaging |
Het |
| Aldh6a1 |
A |
G |
12: 84,483,157 (GRCm39) |
V390A |
probably damaging |
Het |
| Alox5 |
T |
C |
6: 116,437,927 (GRCm39) |
D20G |
probably damaging |
Het |
| Atp2a2 |
A |
T |
5: 122,600,009 (GRCm39) |
F487I |
probably damaging |
Het |
| BC048679 |
G |
A |
7: 81,145,091 (GRCm39) |
T84M |
probably damaging |
Het |
| C2cd3 |
T |
C |
7: 100,039,373 (GRCm39) |
S191P |
probably benign |
Het |
| Cdh6 |
A |
G |
15: 13,064,497 (GRCm39) |
V131A |
probably benign |
Het |
| Chrna9 |
A |
G |
5: 66,134,423 (GRCm39) |
T425A |
probably benign |
Het |
| Cplane2 |
T |
C |
4: 140,947,158 (GRCm39) |
Y180H |
probably damaging |
Het |
| Ddx39a |
A |
G |
8: 84,448,440 (GRCm39) |
S231G |
probably benign |
Het |
| Diaph1 |
C |
T |
18: 37,984,688 (GRCm39) |
G1176R |
probably damaging |
Het |
| Dnah10 |
G |
T |
5: 124,864,484 (GRCm39) |
V2230L |
probably benign |
Het |
| Foxo1 |
T |
C |
3: 52,176,676 (GRCm39) |
S152P |
probably damaging |
Het |
| Fras1 |
T |
A |
5: 96,805,109 (GRCm39) |
D1250E |
probably benign |
Het |
| G6pd2 |
A |
G |
5: 61,966,785 (GRCm39) |
I187V |
probably benign |
Het |
| Gm10113 |
T |
C |
13: 46,330,992 (GRCm39) |
|
noncoding transcript |
Het |
| Hoxd1 |
A |
G |
2: 74,593,792 (GRCm39) |
D116G |
probably damaging |
Het |
| Igkv13-85 |
A |
T |
6: 68,907,544 (GRCm39) |
I19K |
probably benign |
Het |
| Jag2 |
C |
T |
12: 112,880,486 (GRCm39) |
V288M |
probably damaging |
Het |
| Ndrg2 |
A |
G |
14: 52,148,541 (GRCm39) |
|
probably null |
Het |
| Neurl3 |
G |
A |
1: 36,308,501 (GRCm39) |
Q104* |
probably null |
Het |
| Nudt16l1 |
C |
T |
16: 4,757,485 (GRCm39) |
R133W |
probably damaging |
Het |
| Oasl2 |
A |
T |
5: 115,043,122 (GRCm39) |
Q298L |
possibly damaging |
Het |
| Or3a10 |
A |
T |
11: 73,935,848 (GRCm39) |
M84K |
possibly damaging |
Het |
| Or51a25 |
C |
T |
7: 102,373,483 (GRCm39) |
M71I |
probably benign |
Het |
| Pnma2 |
C |
A |
14: 67,153,746 (GRCm39) |
Q57K |
probably benign |
Het |
| Pramel22 |
A |
T |
4: 143,382,181 (GRCm39) |
L172I |
probably benign |
Het |
| Rps7 |
T |
A |
12: 28,681,136 (GRCm39) |
E188D |
probably benign |
Het |
| Rrp1b |
T |
C |
17: 32,270,677 (GRCm39) |
V212A |
possibly damaging |
Het |
| Serpina9 |
C |
A |
12: 103,974,644 (GRCm39) |
A170S |
probably benign |
Het |
| Shmt2 |
C |
T |
10: 127,354,789 (GRCm39) |
V299I |
probably benign |
Het |
| Siae |
C |
T |
9: 37,556,148 (GRCm39) |
P435S |
probably damaging |
Het |
| Sntb1 |
C |
G |
15: 55,506,191 (GRCm39) |
G461R |
probably damaging |
Het |
| Stimate |
T |
A |
14: 30,547,793 (GRCm39) |
F36I |
probably damaging |
Het |
| Tas2r124 |
T |
C |
6: 132,732,503 (GRCm39) |
Y271H |
possibly damaging |
Het |
| Thsd7a |
A |
T |
6: 12,327,582 (GRCm39) |
I1430K |
probably damaging |
Het |
| Trmt9b |
A |
G |
8: 36,979,084 (GRCm39) |
K229R |
probably benign |
Het |
| Tsc22d2 |
T |
A |
3: 58,323,360 (GRCm39) |
V84E |
possibly damaging |
Het |
| Ube2s |
C |
T |
7: 4,813,434 (GRCm39) |
R110Q |
possibly damaging |
Het |
| Usp3 |
C |
T |
9: 66,434,432 (GRCm39) |
C283Y |
probably damaging |
Het |
| Vmn2r81 |
T |
A |
10: 79,129,309 (GRCm39) |
Y733* |
probably null |
Het |
| Wdr75 |
T |
A |
1: 45,856,487 (GRCm39) |
C503* |
probably null |
Het |
| Zfp764 |
T |
C |
7: 127,004,541 (GRCm39) |
M197V |
probably benign |
Het |
|
| Other mutations in Smarcal1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01358:Smarcal1
|
APN |
1 |
72,655,724 (GRCm39) |
missense |
possibly damaging |
0.80 |
|
IGL01658:Smarcal1
|
APN |
1 |
72,625,290 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL01980:Smarcal1
|
APN |
1 |
72,655,679 (GRCm39) |
nonsense |
probably null |
|
|
IGL02007:Smarcal1
|
APN |
1 |
72,635,099 (GRCm39) |
missense |
probably damaging |
0.98 |
|
IGL02153:Smarcal1
|
APN |
1 |
72,672,214 (GRCm39) |
utr 3 prime |
probably benign |
|
|
IGL02496:Smarcal1
|
APN |
1 |
72,659,247 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03084:Smarcal1
|
APN |
1 |
72,638,094 (GRCm39) |
splice site |
probably null |
|
|
IGL03135:Smarcal1
|
APN |
1 |
72,655,660 (GRCm39) |
splice site |
probably null |
|
|
IGL03306:Smarcal1
|
APN |
1 |
72,665,625 (GRCm39) |
missense |
probably benign |
0.12 |
|
R0133:Smarcal1
|
UTSW |
1 |
72,672,010 (GRCm39) |
missense |
probably benign |
0.05 |
|
R0315:Smarcal1
|
UTSW |
1 |
72,634,970 (GRCm39) |
nonsense |
probably null |
|
|
R0396:Smarcal1
|
UTSW |
1 |
72,665,632 (GRCm39) |
missense |
probably benign |
0.03 |
|
R0891:Smarcal1
|
UTSW |
1 |
72,638,015 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1799:Smarcal1
|
UTSW |
1 |
72,625,120 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R1854:Smarcal1
|
UTSW |
1 |
72,625,258 (GRCm39) |
missense |
possibly damaging |
0.77 |
|
R3725:Smarcal1
|
UTSW |
1 |
72,665,755 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R3726:Smarcal1
|
UTSW |
1 |
72,665,755 (GRCm39) |
missense |
possibly damaging |
0.88 |
|
R4164:Smarcal1
|
UTSW |
1 |
72,665,848 (GRCm39) |
intron |
probably benign |
|
|
R4438:Smarcal1
|
UTSW |
1 |
72,650,637 (GRCm39) |
intron |
probably benign |
|
|
R4722:Smarcal1
|
UTSW |
1 |
72,650,496 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4796:Smarcal1
|
UTSW |
1 |
72,636,599 (GRCm39) |
missense |
probably benign |
|
|
R4989:Smarcal1
|
UTSW |
1 |
72,672,019 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
R5367:Smarcal1
|
UTSW |
1 |
72,635,135 (GRCm39) |
critical splice donor site |
probably null |
|
|
R5418:Smarcal1
|
UTSW |
1 |
72,638,068 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5430:Smarcal1
|
UTSW |
1 |
72,665,776 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5591:Smarcal1
|
UTSW |
1 |
72,630,412 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5607:Smarcal1
|
UTSW |
1 |
72,625,372 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5809:Smarcal1
|
UTSW |
1 |
72,630,296 (GRCm39) |
missense |
probably benign |
0.09 |
|
R6395:Smarcal1
|
UTSW |
1 |
72,655,716 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R6447:Smarcal1
|
UTSW |
1 |
72,625,033 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R6852:Smarcal1
|
UTSW |
1 |
72,630,332 (GRCm39) |
missense |
possibly damaging |
0.75 |
|
R7060:Smarcal1
|
UTSW |
1 |
72,652,101 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7692:Smarcal1
|
UTSW |
1 |
72,625,179 (GRCm39) |
missense |
probably benign |
0.08 |
|
R7975:Smarcal1
|
UTSW |
1 |
72,652,150 (GRCm39) |
missense |
probably benign |
0.08 |
|
R8232:Smarcal1
|
UTSW |
1 |
72,665,722 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8407:Smarcal1
|
UTSW |
1 |
72,640,554 (GRCm39) |
missense |
probably benign |
0.04 |
|
R8901:Smarcal1
|
UTSW |
1 |
72,624,939 (GRCm39) |
missense |
possibly damaging |
0.71 |
|
R9329:Smarcal1
|
UTSW |
1 |
72,665,697 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R9548:Smarcal1
|
UTSW |
1 |
72,671,999 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
Z1177:Smarcal1
|
UTSW |
1 |
72,630,426 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- AAGCCTCAGTTAAAGGATGCTCG -3'
(R):5'- TCATAGATCGCACAGAGATTGG -3'
Sequencing Primer
(F):5'- CCTCAGTTAAAGGATGCTCGTAAGC -3'
(R):5'- ACAGAGATTGGTCACTTGCC -3'
|
| Posted On |
2016-07-06 |
Incidental Mutation