Mutagenetix > Incidental Mutation

Incidental Mutation 'R9548:Smarcal1'

720216

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 #

R9548 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

72622410-72672293 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 72671999 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 840 (I840T)

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

possibly damaging
Transcript: ENSMUST00000047615
AA Change: I840T

PolyPhen 2 Score 0.843 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000047589
Gene: ENSMUSG00000039354
AA Change: I840T

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

possibly damaging
Transcript: ENSMUST00000152225
AA Change: I840T

PolyPhen 2 Score 0.843 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000137833
Gene: ENSMUSG00000039354
AA Change: I840T

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: 99.9%
10x: 99.3%
20x: 97.5%

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ankfy1	G	A	11: 72,641,005 (GRCm39)		probably null	Het
Arid1b	A	G	17: 5,385,262 (GRCm39)	Y1340C	probably damaging	Het
Bcl2	C	A	1: 106,640,508 (GRCm39)	A35S	probably benign	Het
Brf2	A	T	8: 27,614,623 (GRCm39)	S188T	probably benign	Het
Carmil1	C	A	13: 24,460,516 (GRCm39)	G21V	probably damaging	Het
Cavin4	T	C	4: 48,663,956 (GRCm39)	V112A	probably benign	Het
Cd300lf	T	C	11: 115,007,858 (GRCm39)	E319G	probably benign	Het
Cd44	A	T	2: 102,661,832 (GRCm39)	D587E	possibly damaging	Het
Cfap53	A	T	18: 74,438,040 (GRCm39)	T239S	possibly damaging	Het
Cma2	A	C	14: 56,211,256 (GRCm39)	I239L	probably damaging	Het
Cnot1	A	T	8: 96,482,854 (GRCm39)	M733K	probably benign	Het
Cyp2f2	A	G	7: 26,829,170 (GRCm39)	D225G	probably benign	Het
Cyp4f40	G	A	17: 32,890,158 (GRCm39)	R276H	probably benign	Het
Cytip	A	T	2: 58,041,141 (GRCm39)	F88L	probably damaging	Het
Dnaaf2	T	C	12: 69,244,776 (GRCm39)	N95S	probably damaging	Het
Dnah5	C	A	15: 28,328,025 (GRCm39)	T2133K	possibly damaging	Het
Dusp9	TAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCTAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCTAAAGCGGAGGCCAAAGCGGAGGCCAAAG	TAAAGCGGAGGCCAAAGCGGAGGCCAAAGCGGAGGCTAAAGCGGAGGCCAAAGCGGAGGCCAAAG	X: 72,684,217 (GRCm39)		probably benign	Het
Elapor2	G	A	5: 9,490,859 (GRCm39)	G623D	probably damaging	Het
Epn2	A	T	11: 61,436,988 (GRCm39)	S195T	probably benign	Het
Exoc3	A	T	13: 74,330,285 (GRCm39)	Y521N	possibly damaging	Het
Fbxo10	C	A	4: 45,058,970 (GRCm39)	V256L	probably damaging	Het
Fis1	A	T	5: 136,991,907 (GRCm39)	T34S	probably benign	Het
Gm10309	A	T	17: 86,806,161 (GRCm39)	C118S	unknown	Het
Grip1	G	A	10: 119,874,569 (GRCm39)	E778K	possibly damaging	Het
Hook1	T	A	4: 95,891,808 (GRCm39)	V340E	probably damaging	Het
Ifng	C	A	10: 118,277,128 (GRCm39)	H23Q	probably benign	Het
Lect2	C	T	13: 56,694,660 (GRCm39)	E32K	probably benign	Het
Lrp1	T	G	10: 127,388,733 (GRCm39)	T3239P	probably damaging	Het
Lrrc14b	T	A	13: 74,511,996 (GRCm39)	Y28F	probably benign	Het
Maml3	A	T	3: 51,763,791 (GRCm39)	V391E	possibly damaging	Het
Map3k8	C	T	18: 4,349,141 (GRCm39)	R59H	probably benign	Het
Med1	G	T	11: 98,070,884 (GRCm39)	L120I	possibly damaging	Het
Muc5b	C	A	7: 141,421,648 (GRCm39)	H4349N	possibly damaging	Het
Myo1h	C	T	5: 114,499,154 (GRCm39)	P110S	probably benign	Het
Nol10	T	G	12: 17,466,144 (GRCm39)	I513S	possibly damaging	Het
Nphs1	C	T	7: 30,180,875 (GRCm39)	S1093F	probably benign	Het
Or12e10	A	T	2: 87,641,097 (GRCm39)	N311I	probably damaging	Het
Or4b1b	T	C	2: 90,111,991 (GRCm39)	*309W	probably null	Het
Or56b1b	A	T	7: 108,164,334 (GRCm39)	S223T	possibly damaging	Het
Or5p72	A	T	7: 108,022,416 (GRCm39)	T213S	possibly damaging	Het
Or5w8	A	T	2: 87,688,040 (GRCm39)	I174F	probably damaging	Het
Pcdh17	A	T	14: 84,685,402 (GRCm39)	Y623F	possibly damaging	Het
Pdzd8	T	A	19: 59,289,826 (GRCm39)	I525F	probably benign	Het
Peak1	G	T	9: 56,113,917 (GRCm39)	Q1675K	probably benign	Het
Perm1	T	C	4: 156,302,290 (GRCm39)	V278A	probably benign	Het
Ppp2r5d	G	A	17: 46,998,527 (GRCm39)	R115C	probably damaging	Het
Rnf169	A	T	7: 99,574,690 (GRCm39)	L635Q	probably damaging	Het
Sacs	A	G	14: 61,440,692 (GRCm39)	T913A	probably benign	Het
Sh3bp1	A	T	15: 78,788,673 (GRCm39)	I233F	possibly damaging	Het
Skint9	T	G	4: 112,276,346 (GRCm39)	L8F	probably benign	Het
Slc1a4	A	T	11: 20,258,041 (GRCm39)	N360K	probably damaging	Het
Slc22a16	T	A	10: 40,460,865 (GRCm39)	Y243*	probably null	Het
Slc22a19	C	A	19: 7,659,219 (GRCm39)		probably null	Het
Spata13	A	G	14: 60,991,303 (GRCm39)	K1019E	possibly damaging	Het
Steap1	A	G	5: 5,790,700 (GRCm39)	S83P	possibly damaging	Het
Synj2bp	T	C	12: 81,551,382 (GRCm39)	H78R	probably damaging	Het
Tcstv7a	T	A	13: 120,289,924 (GRCm39)	I91F	probably benign	Het
Tjp3	T	C	10: 81,113,833 (GRCm39)	E475G	probably damaging	Het
Top3a	A	G	11: 60,644,768 (GRCm39)	V312A	probably benign	Het
Traip	C	A	9: 107,833,099 (GRCm39)	T45N	probably damaging	Het
Ttn	T	C	2: 76,573,691 (GRCm39)	Y25734C	probably damaging	Het
Unc79	T	A	12: 102,977,495 (GRCm39)	V166D	probably damaging	Het
Urgcp	C	A	11: 5,667,622 (GRCm39)	V282F	possibly damaging	Het
Vmn1r184	G	A	7: 25,966,734 (GRCm39)	S160N	probably benign	Het
Wdfy3	T	C	5: 102,033,059 (GRCm39)	D2231G	probably damaging	Het
Zan	C	T	5: 137,401,323 (GRCm39)	G4132D	unknown	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
R9329:Smarcal1	UTSW	1	72,665,697 (GRCm39)	missense	probably damaging	0.99
Z1177:Smarcal1	UTSW	1	72,630,426 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TCGAAGAGCAGCATCTTTGTTG -3'
(R):5'- AATCTGCTTTTCTTTGGCGGAC -3'

Sequencing Primer
(F):5'- TTATCTCCTGCCAGTGAGGAGC -3'
(R):5'- GGACTGCCTTCGTCTTCATCTAAGAG -3'

Posted On

2022-07-18