Mutagenetix > Incidental Mutation

Incidental Mutation 'R6395:Smarcal1'

514688

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

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6395 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

72622410-72672293 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 72655716 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Valine at position 665 (E665V)

Ref Sequence

ENSEMBL: ENSMUSP00000137833 (fasta)

Gene Model

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

AlphaFold

Q8BJL0

Predicted Effect

possibly damaging
Transcript: ENSMUST00000047615
AA Change: E665V

PolyPhen 2 Score 0.817 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000047589
Gene: ENSMUSG00000039354
AA Change: E665V

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

noncoding transcript
Transcript: ENSMUST00000136498

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150725

Predicted Effect

possibly damaging
Transcript: ENSMUST00000152225
AA Change: E665V

PolyPhen 2 Score 0.817 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000137833
Gene: ENSMUSG00000039354
AA Change: E665V

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: 99.6%
20x: 98.3%

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: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Actc1	C	A	2: 113,879,731 (GRCm39)	E243*	probably null	Het
Ahi1	T	C	10: 20,855,491 (GRCm39)	I600T	possibly damaging	Het
Apob	A	G	12: 8,058,507 (GRCm39)	T2330A	probably benign	Het
Cabin1	A	T	10: 75,582,576 (GRCm39)	M280K	probably benign	Het
Ccdc117	T	C	11: 5,484,762 (GRCm39)		probably null	Het
Cct8	G	T	16: 87,283,364 (GRCm39)	Y292*	probably null	Het
Celf1	A	G	2: 90,834,203 (GRCm39)	I165V	probably benign	Het
Cenpc1	A	T	5: 86,183,429 (GRCm39)	N453K	probably benign	Het
Chst10	T	C	1: 38,910,770 (GRCm39)	I131M	probably damaging	Het
Cltc	A	G	11: 86,616,006 (GRCm39)	I420T	probably damaging	Het
Cspg4b	T	G	13: 113,506,003 (GRCm39)	C2377W	probably damaging	Het
Dact3	A	C	7: 16,617,086 (GRCm39)	Q95P	probably damaging	Het
Dennd2c	T	C	3: 103,056,540 (GRCm39)		probably null	Het
Dock2	G	T	11: 34,182,874 (GRCm39)	H1586Q	probably damaging	Het
Dst	T	C	1: 34,221,771 (GRCm39)	M2525T	probably benign	Het
Egflam	T	C	15: 7,261,176 (GRCm39)	H786R	probably damaging	Het
Eml6	T	C	11: 29,759,321 (GRCm39)	T811A	probably benign	Het
Epha1	T	C	6: 42,343,106 (GRCm39)	T148A	probably damaging	Het
Fsip1	A	C	2: 118,067,406 (GRCm39)	S306A	probably damaging	Het
Gga2	A	T	7: 121,607,661 (GRCm39)		probably null	Het
Gm10801	C	CGTT	2: 98,494,152 (GRCm39)		probably benign	Het
Gm9837	T	A	11: 53,360,885 (GRCm39)		probably benign	Het
Gnl2	A	T	4: 124,940,058 (GRCm39)	Q310L	probably damaging	Het
H2-M1	T	C	17: 36,982,701 (GRCm39)	D53G	probably benign	Het
Hmcn2	T	A	2: 31,259,269 (GRCm39)	D1036E	probably damaging	Het
Htr3a	A	T	9: 48,811,871 (GRCm39)	D381E	probably benign	Het
Igdcc4	G	A	9: 65,042,400 (GRCm39)	G106R	probably damaging	Het
Igfbp2	A	G	1: 72,864,078 (GRCm39)	T114A	probably damaging	Het
Ints14	A	G	9: 64,885,406 (GRCm39)		probably null	Het
Kcnt1	T	A	2: 25,799,251 (GRCm39)	M906K	possibly damaging	Het
Kif13a	C	T	13: 46,905,931 (GRCm39)	V671M	possibly damaging	Het
Lars2	A	G	9: 123,200,990 (GRCm39)	Q18R	probably benign	Het
Mndal	C	T	1: 173,698,999 (GRCm39)	C222Y	possibly damaging	Het
Msto1	C	T	3: 88,812,781 (GRCm39)	A1854V	possibly damaging	Het
Musk	G	A	4: 58,286,169 (GRCm39)	G20R	probably benign	Het
Or6c215	G	T	10: 129,638,013 (GRCm39)	P127Q	probably damaging	Het
Oxct1	G	T	15: 4,056,309 (GRCm39)	S19I	possibly damaging	Het
Papss2	G	A	19: 32,641,876 (GRCm39)	G517D	probably damaging	Het
Parp14	T	C	16: 35,676,918 (GRCm39)	S1017G	probably benign	Het
Pde2a	A	G	7: 101,150,242 (GRCm39)	Q227R	probably benign	Het
Pdlim5	G	T	3: 142,020,183 (GRCm39)	P92Q	probably damaging	Het
Pkd1l3	C	T	8: 110,350,595 (GRCm39)	T480I	probably benign	Het
Pla2g4c	C	T	7: 13,077,933 (GRCm39)	T357I	probably benign	Het
Ppp3ca	A	G	3: 136,583,531 (GRCm39)	R213G	possibly damaging	Het
Pramel18	G	A	4: 101,767,189 (GRCm39)	R146H	probably benign	Het
Prrc1	C	T	18: 57,495,619 (GRCm39)	S32L	probably null	Het
Prss47	C	T	13: 65,197,116 (GRCm39)	V207I	probably benign	Het
Prtg	G	A	9: 72,819,414 (GRCm39)	V1136I	possibly damaging	Het
Psmb8	T	A	17: 34,418,265 (GRCm39)	M69K	possibly damaging	Het
Rb1	A	T	14: 73,436,636 (GRCm39)	D876E	probably damaging	Het
Rnasel	T	C	1: 153,637,867 (GRCm39)	M680T	probably damaging	Het
Rnf111	G	T	9: 70,383,692 (GRCm39)	N80K	possibly damaging	Het
Senp1	C	T	15: 97,946,074 (GRCm39)	C557Y	probably damaging	Het
Serpina3a	A	T	12: 104,082,710 (GRCm39)	Y161F	probably damaging	Het
Serpinb11	A	T	1: 107,299,781 (GRCm39)		probably null	Het
Sgpl1	C	A	10: 60,947,936 (GRCm39)		probably null	Het
Slc37a4	A	G	9: 44,310,576 (GRCm39)	Y60C	probably damaging	Het
Slc38a10	A	G	11: 120,015,208 (GRCm39)	S381P	probably benign	Het
Slc5a7	C	T	17: 54,585,849 (GRCm39)	V323I	probably damaging	Het
Slco1a7	T	A	6: 141,668,818 (GRCm39)		probably null	Het
Specc1	C	A	11: 62,023,164 (GRCm39)	N736K	probably damaging	Het
Tas2r121	T	C	6: 132,677,495 (GRCm39)	Y159C	probably benign	Het
Tex54	A	G	19: 8,718,462 (GRCm39)	D68G	probably benign	Het
Trank1	A	G	9: 111,196,268 (GRCm39)	I1431V	probably damaging	Het
Ttll6	T	C	11: 96,047,414 (GRCm39)	V671A	probably benign	Het
Ttn	A	T	2: 76,748,931 (GRCm39)		probably benign	Het
Uimc1	T	C	13: 55,188,389 (GRCm39)	T557A	possibly damaging	Het
Uri1	C	A	7: 37,661,974 (GRCm39)	V446L	probably benign	Het
Vpreb1b	C	T	16: 17,798,771 (GRCm39)	R86C	probably damaging	Het
Vwa8	A	G	14: 79,331,184 (GRCm39)	K1231E	probably benign	Het
Xcr1	G	A	9: 123,684,854 (GRCm39)	R303C	probably damaging	Het
Zfp619	C	A	7: 39,186,454 (GRCm39)	A828E	possibly damaging	Het
Zfp687	T	C	3: 94,915,049 (GRCm39)	S1151G	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
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
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'- AGTGATGTTTTGAAATGTACCAGAC -3'
(R):5'- TCAACAGCAGTGAGGTTGTAC -3'

Sequencing Primer
(F):5'- ATGTACCAGACTAGAGTAGTTGC -3'
(R):5'- GGCAACATCAGGCATCTTCCTTAG -3'

Posted On

2018-05-04