Mutagenetix > Incidental Mutation

Incidental Mutation 'R1854:Smarcal1'

205867

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

039878-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1854 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

72622410-72672293 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 72625258 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Aspartic acid at position 135 (G135D)

Ref Sequence

ENSEMBL: ENSMUSP00000137833 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047615] [ENSMUST00000133123] [ENSMUST00000145868] [ENSMUST00000152225]

AlphaFold

Q8BJL0

Predicted Effect

possibly damaging
Transcript: ENSMUST00000047615
AA Change: G135D

PolyPhen 2 Score 0.770 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000047589
Gene: ENSMUSG00000039354
AA Change: G135D

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

SMART Domains

Protein: ENSMUSP00000114848
Gene: ENSMUSG00000039354

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

probably benign
Transcript: ENSMUST00000145868

SMART Domains

Protein: ENSMUSP00000120230
Gene: ENSMUSG00000039354

Domain	Start	End	E-Value	Type
low complexity region	31	51	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150725

Predicted Effect

possibly damaging
Transcript: ENSMUST00000152225
AA Change: G135D

PolyPhen 2 Score 0.770 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000137833
Gene: ENSMUSG00000039354
AA Change: G135D

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: 97.5%
3x: 96.9%
10x: 95.3%
20x: 92.5%

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: 113 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310061N02Rik	C	T	16: 88,504,668 (GRCm39)	R43K	possibly damaging	Het
Acp1	A	G	12: 30,947,804 (GRCm39)	I78T	possibly damaging	Het
Afap1l1	G	T	18: 61,876,365 (GRCm39)	D417E	probably benign	Het
Agap2	G	A	10: 126,916,385 (GRCm39)	V299I	unknown	Het
Ahnak	C	T	19: 8,991,196 (GRCm39)	A4160V	possibly damaging	Het
Anapc1	T	C	2: 128,517,810 (GRCm39)	E278G	probably damaging	Het
Atad2	G	A	15: 57,960,685 (GRCm39)	P971L	possibly damaging	Het
Atg2a	A	G	19: 6,302,461 (GRCm39)	E928G	probably benign	Het
Atp2b2	A	C	6: 113,819,244 (GRCm39)	N16K	probably damaging	Het
Atp6ap1l	T	C	13: 91,031,707 (GRCm39)	E325G	probably damaging	Het
Bfsp2	C	T	9: 103,327,030 (GRCm39)	G236S	probably benign	Het
Ccar1	A	T	10: 62,600,296 (GRCm39)	I545N	probably damaging	Het
Ccser2	A	G	14: 36,640,548 (GRCm39)	C11R	possibly damaging	Het
Cdc42bpg	A	T	19: 6,370,837 (GRCm39)	H1310L	possibly damaging	Het
Ces1h	T	C	8: 94,085,450 (GRCm39)	K339E	probably benign	Het
Cfap91	T	C	16: 38,144,659 (GRCm39)		probably null	Het
Cit	A	G	5: 116,011,960 (GRCm39)	Y189C	probably damaging	Het
Cnih3	C	A	1: 181,282,186 (GRCm39)	S140*	probably null	Het
Cntrl	A	G	2: 35,012,696 (GRCm39)	D278G	probably damaging	Het
Col24a1	G	A	3: 145,164,895 (GRCm39)	G1033D	probably damaging	Het
Col6a1	T	G	10: 76,557,783 (GRCm39)	Y151S	probably damaging	Het
Col6a2	T	A	10: 76,450,646 (GRCm39)	Q95L	probably damaging	Het
Cpd	G	T	11: 76,677,164 (GRCm39)	P1185Q	probably damaging	Het
Cycs	T	A	6: 50,542,309 (GRCm39)	I76F	possibly damaging	Het
Cyp4f16	T	A	17: 32,756,073 (GRCm39)	I34N	probably damaging	Het
Ddx1	A	C	12: 13,279,332 (GRCm39)	S436A	probably benign	Het
Defa30	A	G	8: 21,625,500 (GRCm39)	Y88C	probably damaging	Het
Dhx30	G	A	9: 109,917,740 (GRCm39)	L317F	probably damaging	Het
Dll3	C	A	7: 27,995,835 (GRCm39)	G322V	probably damaging	Het
Dnah10	G	A	5: 124,881,753 (GRCm39)	D2843N	probably damaging	Het
Dnaja3	C	T	16: 4,515,133 (GRCm39)	T266I	probably damaging	Het
Dpp9	T	C	17: 56,509,885 (GRCm39)	I314V	probably benign	Het
E030025P04Rik	A	G	11: 109,034,744 (GRCm39)	V48A	unknown	Het
Enpp2	C	T	15: 54,709,219 (GRCm39)	E803K	probably damaging	Het
Eri3	G	A	4: 117,506,562 (GRCm39)	G297D	probably benign	Het
Esp34	A	G	17: 38,870,424 (GRCm39)	E38G	possibly damaging	Het
Fabp3	C	T	4: 130,206,180 (GRCm39)	T57I	probably benign	Het
Frzb	A	G	2: 80,276,724 (GRCm39)	V154A	possibly damaging	Het
Fsip2	G	T	2: 82,823,601 (GRCm39)	A6445S	possibly damaging	Het
Gm11938	G	A	11: 99,493,843 (GRCm39)	T84I	possibly damaging	Het
Gm4787	T	A	12: 81,425,108 (GRCm39)	H350L	probably damaging	Het
Gpa33	A	G	1: 165,992,759 (GRCm39)	I291V	probably benign	Het
Gpr158	A	G	2: 21,373,935 (GRCm39)	Y290C	probably damaging	Het
Gpsm1	G	T	2: 26,234,725 (GRCm39)	G84W	probably damaging	Het
Hormad1	A	G	3: 95,487,317 (GRCm39)	N267S	probably benign	Het
Htr2a	A	T	14: 74,943,193 (GRCm39)	I258F	probably damaging	Het
Htra4	T	C	8: 25,523,597 (GRCm39)	T323A	probably damaging	Het
Ift140	T	A	17: 25,254,813 (GRCm39)	F162Y	probably benign	Het
Islr2	T	C	9: 58,107,099 (GRCm39)	T54A	probably damaging	Het
Kcna4	T	G	2: 107,126,829 (GRCm39)	V521G	probably damaging	Het
Kdr	C	T	5: 76,113,565 (GRCm39)	G768S	possibly damaging	Het
Kif6	G	T	17: 50,208,799 (GRCm39)	A740S	probably benign	Het
Lad1	T	A	1: 135,755,468 (GRCm39)	V248E	probably damaging	Het
Lamb1	T	G	12: 31,368,271 (GRCm39)	C1134G	probably damaging	Het
Lamc1	A	G	1: 153,125,618 (GRCm39)	Y552H	probably damaging	Het
Mctp1	A	T	13: 76,973,860 (GRCm39)	T706S	probably damaging	Het
Med12l	A	G	3: 59,168,193 (GRCm39)	Y1541C	probably damaging	Het
Mnx1	C	T	5: 29,682,780 (GRCm39)	S165N	unknown	Het
Morn3	A	T	5: 123,184,692 (GRCm39)		probably null	Het
Nalcn	C	T	14: 123,697,824 (GRCm39)	R484Q	probably damaging	Het
Nr4a1	T	C	15: 101,169,645 (GRCm39)	I305T	probably benign	Het
Or1j11	C	T	2: 36,311,886 (GRCm39)	H159Y	probably damaging	Het
Or2z2	G	A	11: 58,346,257 (GRCm39)	R173W	probably damaging	Het
Pabir2	T	A	X: 52,342,933 (GRCm39)	Q201H	probably benign	Het
Pcdhb5	T	C	18: 37,455,393 (GRCm39)	V591A	possibly damaging	Het
Pdia3	T	C	2: 121,262,144 (GRCm39)	I205T	probably benign	Het
Pdia4	A	T	6: 47,790,161 (GRCm39)	D26E	unknown	Het
Phactr3	C	A	2: 177,924,940 (GRCm39)	L292M	probably damaging	Het
Phf21b	T	A	15: 84,738,963 (GRCm39)	I21F	probably benign	Het
Pign	A	G	1: 105,482,223 (GRCm39)	V791A	probably damaging	Het
Pitpna	A	G	11: 75,499,929 (GRCm39)		probably null	Het
Piwil1	G	T	5: 128,824,903 (GRCm39)	E534*	probably null	Het
Plcz1	T	A	6: 139,938,775 (GRCm39)	I526F	probably benign	Het
Pms2	A	T	5: 143,862,714 (GRCm39)	K607I	probably benign	Het
Pnn	T	A	12: 59,118,399 (GRCm39)	N327K	probably damaging	Het
Pogz	C	T	3: 94,786,160 (GRCm39)	T863I	probably benign	Het
Polq	C	T	16: 36,882,471 (GRCm39)	T1545I	probably benign	Het
Psd4	G	A	2: 24,287,468 (GRCm39)	E467K	probably benign	Het
Pstpip2	T	A	18: 77,959,499 (GRCm39)	L198Q	probably damaging	Het
Pzp	T	C	6: 128,479,188 (GRCm39)	Y655C	probably damaging	Het
Qrsl1	C	T	10: 43,770,541 (GRCm39)	G117E	probably damaging	Het
Rad54b	G	A	4: 11,601,669 (GRCm39)	C408Y	probably damaging	Het
Ralb	T	A	1: 119,403,797 (GRCm39)	Q110L	possibly damaging	Het
Rrm2	A	G	12: 24,763,151 (GRCm39)	K218E	probably damaging	Het
Siglece	A	G	7: 43,309,360 (GRCm39)	F66S	probably benign	Het
Slc17a8	A	T	10: 89,442,627 (GRCm39)	C69S	unknown	Het
Slc1a6	T	A	10: 78,648,758 (GRCm39)	V493E	probably damaging	Het
Slc38a11	A	T	2: 65,193,860 (GRCm39)		probably null	Het
Snrnp70	T	A	7: 45,026,644 (GRCm39)	R242*	probably null	Het
St3gal5	T	C	6: 72,109,077 (GRCm39)	L55P	probably damaging	Het
Sulf1	A	G	1: 12,908,661 (GRCm39)	N558S	probably benign	Het
Supt6	T	C	11: 78,123,366 (GRCm39)	I104V	possibly damaging	Het
Tas2r113	T	A	6: 132,870,292 (GRCm39)	Y107N	probably damaging	Het
Tcf7	A	G	11: 52,147,891 (GRCm39)	V187A	probably benign	Het
Tdrd9	G	A	12: 112,011,246 (GRCm39)	G1152R	probably damaging	Het
Tfpi	A	G	2: 84,288,451 (GRCm39)	Y9H	probably benign	Het
Tnk2	G	A	16: 32,498,960 (GRCm39)	V758I	probably damaging	Het
Trim72	A	G	7: 127,608,254 (GRCm39)	I251V	probably benign	Het
Trip12	T	A	1: 84,705,866 (GRCm39)	N655Y	probably damaging	Het
Ttn	A	G	2: 76,581,773 (GRCm39)	V23040A	probably damaging	Het
Tulp2	T	A	7: 45,167,367 (GRCm39)	N188K	probably damaging	Het
Ube2c	C	T	2: 164,613,282 (GRCm39)	H67Y	probably damaging	Het
Unc80	C	A	1: 66,670,573 (GRCm39)	P1899T	possibly damaging	Het
Usp34	C	T	11: 23,376,153 (GRCm39)	A1879V	probably benign	Het
Vmn2r118	G	A	17: 55,918,556 (GRCm39)	S112L	possibly damaging	Het
Wdfy3	A	T	5: 102,036,052 (GRCm39)	V2122E	probably benign	Het
Zcchc4	A	G	5: 52,973,168 (GRCm39)	Y344C	probably damaging	Het
Zdbf2	GAAAAA	GAAAAAA	1: 63,344,701 (GRCm39)		probably null	Het
Zdhhc25	A	T	15: 88,484,689 (GRCm39)	H8L	probably benign	Het
Zfp455	A	T	13: 67,355,881 (GRCm39)	H383L	probably damaging	Het
Zfp663	A	G	2: 165,195,211 (GRCm39)	I336T	probably benign	Het
Zfp738	T	A	13: 67,818,476 (GRCm39)	H505L	probably damaging	Het
Zfp84	T	G	7: 29,474,796 (GRCm39)	F23V	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
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
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'- TCCTACTGATCAGAGACCTCACAG -3'
(R):5'- GCGATCCCCAGTCTTTATGC -3'

Sequencing Primer
(F):5'- GAGACCTCACAGCTCCCG -3'
(R):5'- CCCCGTAGAAAGCCTGTGTTTTG -3'

Posted On

2014-06-23