Mutagenetix > Incidental Mutation

Incidental Mutation 'R0133:Smarcal1'

21727

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

038418-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0133 (G1)

Quality Score

225

Status

Validated (trace)

Chromosome

Chromosomal Location

72622410-72672293 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 72672010 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 844 (F844L)

Ref Sequence

ENSEMBL: ENSMUSP00000137833 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047615] [ENSMUST00000152225]

AlphaFold

Q8BJL0

Predicted Effect

probably benign
Transcript: ENSMUST00000047615
AA Change: F844L

PolyPhen 2 Score 0.055 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000047589
Gene: ENSMUSG00000039354
AA Change: F844L

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

noncoding transcript
Transcript: ENSMUST00000126832

Predicted Effect

probably benign
Transcript: ENSMUST00000152225
AA Change: F844L

PolyPhen 2 Score 0.055 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000137833
Gene: ENSMUSG00000039354
AA Change: F844L

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

Meta Mutation Damage Score

0.0732

Coding Region Coverage

1x: 98.8%
3x: 97.9%
10x: 95.2%
20x: 89.4%

Validation Efficiency

99% (83/84)

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: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acbd4	T	C	11: 102,996,214 (GRCm39)	S172P	probably damaging	Het
Akap6	A	T	12: 53,186,254 (GRCm39)	K1223*	probably null	Het
Akna	G	A	4: 63,297,598 (GRCm39)	Q819*	probably null	Het
Ankrd2	T	C	19: 42,032,510 (GRCm39)	V257A	probably benign	Het
Arap1	T	A	7: 101,035,436 (GRCm39)	D30E	probably damaging	Het
Atp6v0d2	T	C	4: 19,910,578 (GRCm39)		probably benign	Het
Blm	T	A	7: 80,152,115 (GRCm39)	I611F	possibly damaging	Het
Ccng2	A	G	5: 93,421,240 (GRCm39)	K250R	probably benign	Het
Cdhr3	A	G	12: 33,142,751 (GRCm39)	L8P	possibly damaging	Het
Csf2rb	T	G	15: 78,223,204 (GRCm39)		probably benign	Het
Ctbs	A	G	3: 146,163,223 (GRCm39)	I204V	probably benign	Het
Cxcl16	T	A	11: 70,349,596 (GRCm39)	E76D	possibly damaging	Het
Dhx15	T	C	5: 52,311,414 (GRCm39)	I689V	possibly damaging	Het
Dlk2	T	C	17: 46,609,868 (GRCm39)		probably benign	Het
Dnah2	A	T	11: 69,311,835 (GRCm39)	M4452K	probably damaging	Het
Dok4	T	A	8: 95,591,991 (GRCm39)	I280F	probably benign	Het
Dsc3	T	C	18: 20,104,639 (GRCm39)	T563A	probably damaging	Het
Dsg1b	C	T	18: 20,537,935 (GRCm39)	A617V	probably damaging	Het
Eps8l2	C	T	7: 140,942,120 (GRCm39)	P721S	unknown	Het
Evx2	T	C	2: 74,489,426 (GRCm39)	D112G	possibly damaging	Het
Fam124a	C	A	14: 62,843,782 (GRCm39)	T430K	possibly damaging	Het
Fbrs	C	T	7: 127,088,782 (GRCm39)		probably benign	Het
Fbxw14	T	C	9: 109,103,647 (GRCm39)	T22A	probably benign	Het
Fmo5	T	G	3: 97,552,952 (GRCm39)	V300G	probably damaging	Het
Gadl1	T	C	9: 115,770,411 (GRCm39)	S75P	probably benign	Het
Galnt2	T	G	8: 125,065,277 (GRCm39)	I469S	probably benign	Het
Gga3	T	A	11: 115,479,805 (GRCm39)		probably benign	Het
Gm10647	T	C	9: 66,705,771 (GRCm39)		probably benign	Het
Gm14180	C	A	11: 99,625,043 (GRCm39)	C25F	unknown	Het
Grid2	A	T	6: 64,297,116 (GRCm39)	D493V	probably damaging	Het
Gzmc	T	A	14: 56,469,754 (GRCm39)	Y182F	possibly damaging	Het
Hecw2	A	C	1: 53,869,899 (GRCm39)	L1443R	probably damaging	Het
Igkv4-62	A	G	6: 69,377,053 (GRCm39)	I32T	probably benign	Het
Ikzf1	T	A	11: 11,691,015 (GRCm39)		probably null	Het
Il27ra	G	A	8: 84,760,571 (GRCm39)		probably benign	Het
Jmjd1c	C	A	10: 67,076,587 (GRCm39)	A2137D	probably benign	Het
Kcnc2	T	C	10: 112,294,502 (GRCm39)	C579R	probably damaging	Het
Kdr	T	C	5: 76,112,498 (GRCm39)	T862A	probably damaging	Het
Kif17	T	C	4: 138,005,556 (GRCm39)	S182P	possibly damaging	Het
Klf5	A	T	14: 99,539,318 (GRCm39)	T164S	probably benign	Het
Ksr2	T	G	5: 117,693,359 (GRCm39)	V269G	possibly damaging	Het
Mcm5	T	A	8: 75,847,539 (GRCm39)	D445E	probably damaging	Het
Mlkl	T	C	8: 112,054,580 (GRCm39)	I186V	probably damaging	Het
Muc4	A	T	16: 32,591,978 (GRCm39)	S3017C	possibly damaging	Het
Myo15a	T	C	11: 60,368,676 (GRCm39)	F479L	possibly damaging	Het
Myo6	A	G	9: 80,181,257 (GRCm39)		probably benign	Het
Myom1	T	A	17: 71,354,782 (GRCm39)	V393E	probably damaging	Het
Nup98	T	A	7: 101,788,859 (GRCm39)		probably null	Het
Odf2l	A	G	3: 144,854,302 (GRCm39)	N383S	probably damaging	Het
Olfml3	A	C	3: 103,644,342 (GRCm39)		probably null	Het
Or10q1	T	A	19: 13,727,352 (GRCm39)	I294N	probably damaging	Het
Or7g17	G	A	9: 18,767,925 (GRCm39)	M1I	probably null	Het
Or8g18	A	G	9: 39,149,307 (GRCm39)	Y141H	probably benign	Het
Or8j3b	A	T	2: 86,205,159 (GRCm39)	V199E	possibly damaging	Het
Plxna4	A	T	6: 32,174,009 (GRCm39)	D1195E	probably benign	Het
Ppp1r1a	T	A	15: 103,446,247 (GRCm39)	H20L	probably damaging	Het
Prdm4	A	G	10: 85,746,085 (GRCm39)		probably null	Het
Prom2	A	G	2: 127,380,258 (GRCm39)		probably benign	Het
Rasal3	T	C	17: 32,622,357 (GRCm39)	M1V	probably null	Het
Rhoj	A	G	12: 75,441,194 (GRCm39)		probably null	Het
Rnf40	C	T	7: 127,196,032 (GRCm39)		probably null	Het
Slc15a3	T	C	19: 10,820,614 (GRCm39)	L77P	probably damaging	Het
Slc26a6	T	C	9: 108,738,522 (GRCm39)	V586A	possibly damaging	Het
Slc30a10	T	A	1: 185,187,370 (GRCm39)	L37Q	probably damaging	Het
Slc43a2	T	A	11: 75,454,403 (GRCm39)	M316K	probably benign	Het
Snx19	A	G	9: 30,339,912 (GRCm39)	E350G	possibly damaging	Het
Tecta	T	A	9: 42,278,524 (GRCm39)	T995S	probably benign	Het
Tmc3	T	G	7: 83,261,681 (GRCm39)	N586K	probably damaging	Het
Tmem107	T	A	11: 68,963,239 (GRCm39)		probably benign	Het
Tmem247	A	G	17: 87,225,989 (GRCm39)	Q51R	probably benign	Het
Tmpo	G	T	10: 90,999,900 (GRCm39)		probably benign	Het
Ubr5	T	A	15: 37,996,815 (GRCm39)	T1894S	probably damaging	Het
Vmn2r92	C	T	17: 18,388,219 (GRCm39)	A408V	probably damaging	Het
Xirp2	T	A	2: 67,347,468 (GRCm39)	H3236Q	probably benign	Het
Zfand4	G	A	6: 116,291,700 (GRCm39)	D545N	probably benign	Het
Zkscan3	G	T	13: 21,578,944 (GRCm39)	P155T	possibly damaging	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
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
R5242:Smarcal1	UTSW	1	72,630,242 (GRCm39)	missense	probably benign	0.00
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'- GCACTGCTTACTGCCAGTCTGATG -3'
(R):5'- CCTTGGACTCTTCTGCGTGACAAAC -3'

Sequencing Primer
(F):5'- CAGTCTGATGGCACTGGAG -3'
(R):5'- TTTCTGACCCTGTCAAAAGGGAG -3'

Posted On

2013-04-12