Mutagenetix > Incidental Mutation

Incidental Mutation 'R6450:Smarcd1'

519377

Institutional Source

Beutler Lab

Gene Symbol

Smarcd1

Ensembl Gene

ENSMUSG00000023018

Gene Name

SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1

Synonyms

D15Kz1, Baf60a

MMRRC Submission

044586-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.844) question?

Stock #

R6450 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

99600175-99611872 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 99605766 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 346 (I346V)

Ref Sequence

ENSEMBL: ENSMUSP00000023759 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000023759] [ENSMUST00000163472] [ENSMUST00000228984] [ENSMUST00000229236] [ENSMUST00000229845] [ENSMUST00000230530]

AlphaFold

Q61466

PDB Structure

Solution structure of the SWIB domain of mouse BRG1-associated factor 60a [SOLUTION NMR]

Predicted Effect

possibly damaging
Transcript: ENSMUST00000023759
AA Change: I346V

PolyPhen 2 Score 0.846 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000023759
Gene: ENSMUSG00000023018
AA Change: I346V

Domain	Start	End	E-Value	Type
low complexity region	9	38	N/A	INTRINSIC
low complexity region	103	117	N/A	INTRINSIC
Blast:KISc	124	271	2e-43	BLAST
SWIB	291	370	1.97e-35	SMART
Blast:MYSc	452	498	2e-17	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000163472

SMART Domains

Protein: ENSMUSP00000128823
Gene: ENSMUSG00000091604

Domain	Start	End	E-Value	Type
low complexity region	18	42	N/A	INTRINSIC
low complexity region	44	78	N/A	INTRINSIC
low complexity region	85	93	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000228984

Predicted Effect

possibly damaging
Transcript: ENSMUST00000229236
AA Change: I305V

PolyPhen 2 Score 0.706 (Sensitivity: 0.86; Specificity: 0.92)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000229686

Predicted Effect

probably benign
Transcript: ENSMUST00000229845

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000229968

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000230504

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000230748

Predicted Effect

probably benign
Transcript: ENSMUST00000230530

Coding Region Coverage

1x: 100.0%
3x: 99.8%
10x: 98.5%
20x: 95.1%

Validation Efficiency

97% (68/70)

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, whose members display helicase and ATPase activities and which are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI and has sequence similarity to the yeast Swp73 protein. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca14	C	G	7: 119,815,449 (GRCm39)	N232K	probably benign	Het
Acaca	T	A	11: 84,171,294 (GRCm39)	V5E	probably damaging	Het
Adam18	A	T	8: 25,119,691 (GRCm39)	D529E	probably benign	Het
Adgrb3	T	C	1: 25,459,683 (GRCm39)	T798A	probably benign	Het
Alyref	T	C	11: 120,486,872 (GRCm39)	T130A	probably benign	Het
Arhgap24	A	G	5: 103,044,990 (GRCm39)	S591G	probably benign	Het
Carmil1	C	T	13: 24,220,547 (GRCm39)	G655E	probably damaging	Het
Cdc42bpg	T	A	19: 6,364,518 (GRCm39)		probably null	Het
Clec12a	T	A	6: 129,330,366 (GRCm39)	L48H	probably damaging	Het
Coq2	C	A	5: 100,809,770 (GRCm39)		probably benign	Het
Crb2	C	A	2: 37,683,838 (GRCm39)	F1113L	possibly damaging	Het
Ctla4	A	T	1: 60,951,872 (GRCm39)	M134L	probably benign	Het
Dnase1l1	C	T	X: 73,320,644 (GRCm39)		probably null	Homo
Dync2i1	A	T	12: 116,210,347 (GRCm39)	Y314*	probably null	Het
Efhb	A	G	17: 53,759,632 (GRCm39)	V290A	possibly damaging	Het
Epha8	T	C	4: 136,659,210 (GRCm39)	N843S	probably damaging	Het
Eva1a	A	T	6: 82,069,086 (GRCm39)	I138F	probably damaging	Het
Fat2	T	A	11: 55,180,136 (GRCm39)	I1402F	probably damaging	Het
Fat3	A	T	9: 15,910,466 (GRCm39)	H1845Q	possibly damaging	Het
Gimap8	T	A	6: 48,633,385 (GRCm39)	F401L	probably benign	Het
Gpr162	C	T	6: 124,838,152 (GRCm39)	R166Q	possibly damaging	Het
H2ac8	A	G	13: 23,755,119 (GRCm39)	V55A	probably damaging	Het
Hdac4	G	A	1: 91,912,433 (GRCm39)	P348S	possibly damaging	Het
Hmcn2	T	C	2: 31,251,812 (GRCm39)	V849A	probably benign	Het
Inpp5b	T	A	4: 124,686,045 (GRCm39)	N696K	probably damaging	Het
Kdm5d	G	T	Y: 927,056 (GRCm39)	R598L	probably damaging	Homo
Kidins220	T	C	12: 25,107,190 (GRCm39)	S1548P	probably benign	Het
Kif2b	C	A	11: 91,467,192 (GRCm39)	V364L	probably damaging	Het
Kitl	A	G	10: 99,923,256 (GRCm39)	M1V	probably null	Het
Klra9	G	T	6: 130,155,995 (GRCm39)	Y253*	probably null	Het
Map6	T	C	7: 98,917,245 (GRCm39)	I6T	probably damaging	Het
Mastl	T	C	2: 23,010,941 (GRCm39)	T768A	probably damaging	Het
Mettl16	T	C	11: 74,696,164 (GRCm39)	V335A	probably benign	Het
Mpl	T	C	4: 118,305,897 (GRCm39)		probably null	Het
Myo5c	C	T	9: 75,193,860 (GRCm39)	T1205I	probably benign	Het
Nav2	C	A	7: 49,244,114 (GRCm39)	L2114I	probably damaging	Het
Neb	T	A	2: 52,084,481 (GRCm39)	K5330*	probably null	Het
Nfe2l1	C	T	11: 96,718,161 (GRCm39)	E125K	possibly damaging	Het
Onecut3	A	G	10: 80,331,922 (GRCm39)	K361E	probably damaging	Het
Or4f47	T	A	2: 111,972,725 (GRCm39)	L145*	probably null	Het
Osbpl6	A	G	2: 76,395,174 (GRCm39)	N370S	possibly damaging	Het
Otud4	T	A	8: 80,399,626 (GRCm39)	M780K	probably benign	Het
P2rx4	A	G	5: 122,865,304 (GRCm39)	T310A	possibly damaging	Het
Pcdha11	G	T	18: 37,146,215 (GRCm39)	D769Y	probably damaging	Het
Pcgf6	C	T	19: 47,037,527 (GRCm39)	R124H	probably benign	Het
Pibf1	T	A	14: 99,374,646 (GRCm39)	Y362N	probably damaging	Het
Ppm1g	T	C	5: 31,360,468 (GRCm39)	E422G	probably benign	Het
Prmt8	T	C	6: 127,709,606 (GRCm39)	I85V	possibly damaging	Het
Prss27	A	T	17: 24,263,988 (GRCm39)	K225*	probably null	Het
Rai1	A	T	11: 60,077,429 (GRCm39)	T498S	probably benign	Het
Sbf2	C	A	7: 110,062,070 (GRCm39)	G23V	probably damaging	Het
Sdha	C	T	13: 74,482,412 (GRCm39)		probably null	Het
Sgo2a	C	T	1: 58,042,092 (GRCm39)	Q140*	probably null	Het
Sh3rf3	A	G	10: 58,819,966 (GRCm39)	D259G	probably damaging	Het
Slc27a3	C	A	3: 90,292,777 (GRCm39)	D631Y	probably damaging	Het
Slc7a10	T	C	7: 34,886,015 (GRCm39)	S37P	possibly damaging	Het
Slco6d1	A	G	1: 98,349,192 (GRCm39)	T88A	probably benign	Het
Smad4	A	T	18: 73,810,817 (GRCm39)	S56T	possibly damaging	Het
Spast	C	T	17: 74,675,835 (GRCm39)	P260S	probably benign	Het
Spata31f1e	C	A	4: 42,792,489 (GRCm39)	G548W	probably damaging	Het
Sprr2i	A	T	3: 92,316,017 (GRCm39)		probably benign	Het
Sptbn5	A	G	2: 119,877,616 (GRCm39)		probably benign	Het
Taar9	A	T	10: 23,985,138 (GRCm39)	Y99N	probably damaging	Het
Trappc10	A	T	10: 78,045,284 (GRCm39)	M468K	possibly damaging	Het
Trim66	T	C	7: 109,059,945 (GRCm39)	R814G	probably benign	Het
Tspan31	A	G	10: 126,904,227 (GRCm39)	C157R	probably damaging	Het
Vmn2r90	A	G	17: 17,953,498 (GRCm39)	D554G	possibly damaging	Het
Vmn2r91	A	T	17: 18,305,527 (GRCm39)	D70V	probably damaging	Het
Wdfy4	C	T	14: 32,830,649 (GRCm39)	G928R	probably damaging	Het
Zfp346	G	T	13: 55,261,517 (GRCm39)	K102N	probably damaging	Het
Zmym4	G	A	4: 126,789,099 (GRCm39)	P1002S	probably damaging	Het

Other mutations in Smarcd1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01516:Smarcd1	APN	15	99,610,094 (GRCm39)	missense	probably benign	0.10
IGL01714:Smarcd1	APN	15	99,610,302 (GRCm39)	missense	probably damaging	1.00
IGL02488:Smarcd1	APN	15	99,609,082 (GRCm39)	missense	possibly damaging	0.83
P0021:Smarcd1	UTSW	15	99,610,242 (GRCm39)	splice site	probably benign
R0597:Smarcd1	UTSW	15	99,608,975 (GRCm39)	missense	probably damaging	1.00
R0645:Smarcd1	UTSW	15	99,605,267 (GRCm39)	splice site	probably null
R1531:Smarcd1	UTSW	15	99,605,264 (GRCm39)	missense	probably damaging	1.00
R1661:Smarcd1	UTSW	15	99,605,519 (GRCm39)	critical splice acceptor site	probably null
R1857:Smarcd1	UTSW	15	99,607,295 (GRCm39)	missense	probably damaging	0.97
R3003:Smarcd1	UTSW	15	99,610,065 (GRCm39)	missense	probably damaging	1.00
R4170:Smarcd1	UTSW	15	99,605,812 (GRCm39)	missense	probably damaging	1.00
R4964:Smarcd1	UTSW	15	99,605,862 (GRCm39)	missense	possibly damaging	0.79
R5116:Smarcd1	UTSW	15	99,600,369 (GRCm39)	missense	probably benign	0.00
R5358:Smarcd1	UTSW	15	99,601,128 (GRCm39)	nonsense	probably null
R5559:Smarcd1	UTSW	15	99,601,176 (GRCm39)	critical splice donor site	probably null
R6026:Smarcd1	UTSW	15	99,603,619 (GRCm39)	missense	probably damaging	1.00
R6424:Smarcd1	UTSW	15	99,602,248 (GRCm39)	missense	probably damaging	1.00
R7126:Smarcd1	UTSW	15	99,607,206 (GRCm39)	missense	probably damaging	1.00
R8476:Smarcd1	UTSW	15	99,600,305 (GRCm39)	missense	probably damaging	0.99
R8487:Smarcd1	UTSW	15	99,605,657 (GRCm39)	missense	probably damaging	0.96
R8872:Smarcd1	UTSW	15	99,608,975 (GRCm39)	missense	probably damaging	1.00
X0026:Smarcd1	UTSW	15	99,600,330 (GRCm39)	missense	probably benign	0.13

Predicted Primers

PCR Primer
(F):5'- TCATCCAAGCACTGTGGCAG -3'
(R):5'- ACTCACTGCTCTGTAGGCAG -3'

Sequencing Primer
(F):5'- GCACTGTGGCAGTATATTAAAACAC -3'
(R):5'- GCACACACTCACTGCTCTG -3'

Posted On

2018-05-24