Mutagenetix > Incidental Mutation

Incidental Mutation 'R9329:Smarcal1'

706695

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

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9329 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

72622410-72672293 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 72665697 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 732 (S732P)

Ref Sequence

ENSEMBL: ENSMUSP00000047589 (fasta)

Gene Model

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

AlphaFold

Q8BJL0

PDB Structure

Crystal Structure of SMARCAL1 HARP substrate recognition domain [X-RAY DIFFRACTION]

Predicted Effect

probably damaging
Transcript: ENSMUST00000047615
AA Change: S732P

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000047589
Gene: ENSMUSG00000039354
AA Change: S732P

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 damaging
Transcript: ENSMUST00000152225
AA Change: S732P

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000137833
Gene: ENSMUSG00000039354
AA Change: S732P

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.4%

Validation Efficiency

99% (73/74)

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: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700003E16Rik	T	G	6: 83,133,556 (GRCm39)	M1R	probably null	Het
Acap2	T	C	16: 30,946,238 (GRCm39)	D235G	probably damaging	Het
Adgrv1	C	A	13: 81,647,241 (GRCm39)	V3100F	probably damaging	Het
Aff4	A	G	11: 53,288,686 (GRCm39)	T401A	probably damaging	Het
Apcs	T	C	1: 172,722,391 (GRCm39)	T22A	probably benign	Het
Atf7ip2	T	C	16: 10,059,738 (GRCm39)	V426A	possibly damaging	Het
Bach2	A	G	4: 32,562,175 (GRCm39)	D214G	possibly damaging	Het
Baz2a	C	T	10: 127,960,925 (GRCm39)	A1578V	possibly damaging	Het
Camk1d	T	C	2: 5,449,954 (GRCm39)	I76V	probably benign	Het
Ccdc182	A	T	11: 88,185,324 (GRCm39)	M135L	probably benign	Het
Cd47	C	T	16: 49,716,731 (GRCm39)	T201I		Het
Chodl	T	C	16: 78,746,030 (GRCm39)	S290P	possibly damaging	Het
Chst15	A	G	7: 131,868,520 (GRCm39)	L300P	possibly damaging	Het
Ciita	T	C	16: 10,324,571 (GRCm39)	S168P	probably damaging	Het
Cntn2	C	T	1: 132,456,678 (GRCm39)	V123I	probably benign	Het
Cyld	T	A	8: 89,457,348 (GRCm39)	L527Q	probably benign	Het
Dbn1	T	A	13: 55,631,241 (GRCm39)	Y34F	probably damaging	Het
Enc1	C	A	13: 97,383,018 (GRCm39)	Y509*	probably null	Het
Ermard	A	T	17: 15,273,643 (GRCm39)	E409D	probably benign	Het
Extl3	T	C	14: 65,314,765 (GRCm39)	E139G	possibly damaging	Het
Fa2h	A	T	8: 112,082,115 (GRCm39)	V177E	possibly damaging	Het
Flot2	T	C	11: 77,949,772 (GRCm39)	I367T	probably damaging	Het
Fras1	T	C	5: 96,884,813 (GRCm39)	Y2564H	probably damaging	Het
Fxyd3	A	G	7: 30,773,018 (GRCm39)	V10A	probably benign	Het
Gfra3	A	G	18: 34,837,560 (GRCm39)	L146P	probably damaging	Het
Gm49359	T	C	13: 62,602,448 (GRCm39)	N251D	probably benign	Het
Hps6	A	G	19: 45,992,542 (GRCm39)	S160G	probably benign	Het
Hsd17b7	C	A	1: 169,794,875 (GRCm39)	A55S	probably damaging	Het
Hspa12a	T	C	19: 58,789,298 (GRCm39)	D446G	probably benign	Het
Htt	G	A	5: 34,989,957 (GRCm39)	R1163Q	possibly damaging	Het
Ift81	T	C	5: 122,697,833 (GRCm39)		probably null	Het
Ighv5-15	T	G	12: 113,790,395 (GRCm39)	Y75S	probably benign	Het
Kcnd2	T	A	6: 21,725,981 (GRCm39)	H491Q	probably damaging	Het
Lamb3	C	A	1: 193,014,665 (GRCm39)	T608K	probably benign	Het
Lrtm2	T	A	6: 119,297,412 (GRCm39)	K210*	probably null	Het
Med13	G	T	11: 86,189,283 (GRCm39)	P1209T	probably benign	Het
Mtus1	G	A	8: 41,537,239 (GRCm39)	T159I	probably damaging	Het
Myt1l	A	G	12: 29,901,659 (GRCm39)	M805V	unknown	Het
Neb	G	T	2: 52,160,231 (GRCm39)	L2261I	probably benign	Het
Nlrp4c	G	A	7: 6,068,498 (GRCm39)	R133H	probably benign	Het
Nol11	A	T	11: 107,071,765 (GRCm39)	L276Q	probably damaging	Het
Nrap	A	G	19: 56,350,277 (GRCm39)	Y614H	probably damaging	Het
Or13c9	G	A	4: 52,936,211 (GRCm39)	T24M	probably damaging	Het
Or52p1	A	G	7: 104,267,705 (GRCm39)	H273R	probably damaging	Het
Pou2f3	A	G	9: 43,040,224 (GRCm39)	S355P	probably damaging	Het
Ppm1l	C	A	3: 69,460,453 (GRCm39)	N343K	probably damaging	Het
Prh1	A	T	6: 132,548,573 (GRCm39)	I27F	unknown	Het
Prkrip1	A	T	5: 136,223,203 (GRCm39)	L85Q	probably damaging	Het
Pycr3	C	T	15: 75,790,563 (GRCm39)	V99I	probably benign	Het
R3hdm4	T	A	10: 79,749,393 (GRCm39)	N72I	probably damaging	Het
Rab11fip3	G	T	17: 26,231,032 (GRCm39)	H738N	probably benign	Het
Rtl1	G	A	12: 109,556,673 (GRCm39)	A1722V	possibly damaging	Het
Sell	A	G	1: 163,893,122 (GRCm39)	N113D	probably damaging	Het
Smurf2	A	T	11: 106,743,424 (GRCm39)	D207E	probably benign	Het
Spata31h1	G	A	10: 82,121,439 (GRCm39)	S3857L	probably benign	Het
Tat	C	T	8: 110,723,510 (GRCm39)	R333C	probably benign	Het
Tmem121b	A	T	6: 120,469,234 (GRCm39)	F494L	probably damaging	Het
Tmem198	C	A	1: 75,456,522 (GRCm39)	P89Q	probably damaging	Het
Tnks2	T	G	19: 36,835,284 (GRCm39)	C2G	probably damaging	Het
Trappc9	T	C	15: 72,673,202 (GRCm39)	E869G	unknown	Het
Trim42	T	A	9: 97,251,584 (GRCm39)	K105M	probably benign	Het
Ttll3	T	C	6: 113,369,635 (GRCm39)	S60P	probably benign	Het
Ttll4	T	A	1: 74,725,121 (GRCm39)	I625N	possibly damaging	Het
Tubgcp5	T	A	7: 55,479,181 (GRCm39)		probably null	Het
Txlnb	A	T	10: 17,682,594 (GRCm39)	Y172F	probably damaging	Het
Ube2e3	A	T	2: 78,744,035 (GRCm39)	D88V	possibly damaging	Het
Vmn1r189	T	A	13: 22,286,430 (GRCm39)	I136L	probably benign	Het
Vmn2r71	A	G	7: 85,267,950 (GRCm39)	I135V	probably benign	Het
Vmn2r73	T	A	7: 85,519,073 (GRCm39)	R516S	probably benign	Het
Wrn	C	T	8: 33,731,006 (GRCm39)	E1352K	probably benign	Het
Zfp318	T	C	17: 46,722,139 (GRCm39)	S1381P	probably damaging	Het
Zfp747	A	T	7: 126,973,655 (GRCm39)	Y172N	probably 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
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
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'- CCAACCTTCAGTTTTGTAAAGGG -3'
(R):5'- TGCCATTCATTTACGGATCTTG -3'

Sequencing Primer
(F):5'- CTTCAGTTTTGTAAAGGGAAACAGCC -3'
(R):5'- GGATCTTGTATTTCTCAGCCCTGG -3'

Posted On

2022-04-18