Mutagenetix > Incidental Mutation

Incidental Mutation 'R7077:Smarcd3'

549270

Institutional Source

Beutler Lab

Gene Symbol

Smarcd3

Ensembl Gene

ENSMUSG00000028949

Gene Name

SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3

Synonyms

2210409C08Rik, BAF60C, 1500001J14Rik

MMRRC Submission

045172-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7077 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

24797620-24829649 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 24799960 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Aspartic acid at position 270 (A270D)

Ref Sequence

ENSEMBL: ENSMUSP00000030791 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030791] [ENSMUST00000088295] [ENSMUST00000121863] [ENSMUST00000195943] [ENSMUST00000197318]

AlphaFold

Q6P9Z1

Predicted Effect

probably damaging
Transcript: ENSMUST00000030791
AA Change: A270D

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000030791
Gene: ENSMUSG00000028949
AA Change: A270D

Domain	Start	End	E-Value	Type
low complexity region	40	55	N/A	INTRINSIC
low complexity region	72	89	N/A	INTRINSIC
low complexity region	93	102	N/A	INTRINSIC
Blast:KISc	103	239	5e-41	BLAST
SWIB	259	338	3.6e-29	SMART
Blast:MYSc	420	466	1e-11	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000088295

SMART Domains

Protein: ENSMUSP00000085633
Gene: ENSMUSG00000038181

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
Pfam:Fringe	143	298	3.2e-11	PFAM
Pfam:CHGN	242	755	1.7e-144	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000121863

SMART Domains

Protein: ENSMUSP00000112804
Gene: ENSMUSG00000038181

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
Pfam:Fringe	143	298	3.2e-11	PFAM
Pfam:CHGN	242	755	3e-176	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000195943
AA Change: A241D

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000143437
Gene: ENSMUSG00000028949
AA Change: A241D

Domain	Start	End	E-Value	Type
low complexity region	11	26	N/A	INTRINSIC
low complexity region	43	60	N/A	INTRINSIC
low complexity region	64	73	N/A	INTRINSIC
Blast:KISc	74	210	2e-41	BLAST
SWIB	230	309	2.3e-31	SMART
Blast:MYSc	391	437	8e-12	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000197318

SMART Domains

Protein: ENSMUSP00000143185
Gene: ENSMUSG00000038181

Domain	Start	End	E-Value	Type
Pfam:CHGN	1	74	7.5e-22	PFAM

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

98% (54/55)

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. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam21	C	T	12: 81,605,893 (GRCm39)	C623Y	probably damaging	Het
Ago3	T	C	4: 126,265,325 (GRCm39)	K322R	probably null	Het
Ankrd17	T	C	5: 90,433,723 (GRCm39)	H682R	possibly damaging	Het
Aoah	A	G	13: 21,094,276 (GRCm39)	D187G	probably damaging	Het
Arhgap17	T	C	7: 122,879,231 (GRCm39)	D840G	unknown	Het
AW551984	C	T	9: 39,502,723 (GRCm39)	V650I	probably benign	Het
Bok	T	A	1: 93,616,911 (GRCm39)	Y86N	probably damaging	Het
Ccdc146	T	A	5: 21,510,272 (GRCm39)	N580I	possibly damaging	Het
Ccng2	T	C	5: 93,417,199 (GRCm39)	S72P	possibly damaging	Het
Cfap74	T	G	4: 155,540,134 (GRCm39)	I977S	unknown	Het
Cobl	T	C	11: 12,203,441 (GRCm39)	N1087S	probably benign	Het
Cyp21a1	C	A	17: 35,021,333 (GRCm39)	R346L	probably damaging	Het
Eif4a1	A	C	11: 69,561,490 (GRCm39)	F52L	probably damaging	Het
Eif4ebp2	A	C	10: 61,269,580 (GRCm39)	I120S	probably damaging	Het
Enpp2	A	C	15: 54,764,787 (GRCm39)	D146E	probably benign	Het
Exosc9	T	C	3: 36,607,205 (GRCm39)	Y30H	probably damaging	Het
Fam117a	G	A	11: 95,268,498 (GRCm39)	G300S	probably benign	Het
Focad	C	A	4: 88,328,914 (GRCm39)	A1709E	unknown	Het
Fsd1	G	A	17: 56,300,876 (GRCm39)	R245H	probably damaging	Het
Fsip2	T	C	2: 82,813,496 (GRCm39)	F3272L	probably benign	Het
Gcnt2	G	A	13: 41,013,896 (GRCm39)	M22I	probably benign	Het
Gjd4	T	C	18: 9,280,928 (GRCm39)	E50G	probably damaging	Het
Gm10375	G	T	14: 43,840,427 (GRCm39)	T162K	probably benign	Het
Gm10837	C	G	14: 122,728,142 (GRCm39)	A6G	unknown	Het
Gm4924	T	C	10: 82,215,057 (GRCm39)	F952L	unknown	Het
Heatr1	T	C	13: 12,433,045 (GRCm39)	F1132L	possibly damaging	Het
Hnrnpu	A	G	1: 178,159,756 (GRCm39)	Y442H	unknown	Het
Hp1bp3	C	A	4: 137,966,929 (GRCm39)	T408N	probably damaging	Het
Htra3	A	G	5: 35,825,660 (GRCm39)	V198A	probably damaging	Het
Katnal1	T	C	5: 148,828,547 (GRCm39)	T300A	probably benign	Het
Lipo5	G	T	19: 33,445,170 (GRCm39)	P133Q		Het
Lrp1b	A	T	2: 41,660,858 (GRCm39)	H197Q		Het
Mdc1	C	A	17: 36,156,839 (GRCm39)	A82D	probably damaging	Het
Mstn	A	T	1: 53,103,408 (GRCm39)	D248V	probably benign	Het
Myo1d	C	T	11: 80,565,460 (GRCm39)	E426K	probably damaging	Het
Ola1	G	A	2: 72,972,308 (GRCm39)	T221I	probably damaging	Het
Or52z1	A	G	7: 103,436,593 (GRCm39)	I297T	probably damaging	Het
Or5t7	T	C	2: 86,507,236 (GRCm39)	Y147C	possibly damaging	Het
Or7e166	T	A	9: 19,624,428 (GRCm39)	S102T	probably benign	Het
Or8c20	T	A	9: 38,261,266 (GRCm39)	Y290N	probably damaging	Het
Phldb1	T	C	9: 44,623,201 (GRCm39)	T618A	possibly damaging	Het
Pkd1	T	G	17: 24,810,093 (GRCm39)	W3565G	probably damaging	Het
Prl3a1	A	T	13: 27,460,086 (GRCm39)	N190I	probably benign	Het
Ptk2	G	A	15: 73,093,658 (GRCm39)	P854S	possibly damaging	Het
Ptpn11	C	T	5: 121,281,633 (GRCm39)	R484Q	probably benign	Het
Rapgef4	T	C	2: 72,071,820 (GRCm39)	M900T	probably damaging	Het
Slc1a2	A	T	2: 102,607,855 (GRCm39)	D501V	probably benign	Het
Srgap2	A	G	1: 131,272,187 (GRCm39)	M33T		Het
Tle1	G	C	4: 72,076,612 (GRCm39)	P139A	probably benign	Het
Tmem161b	C	A	13: 84,370,537 (GRCm39)		probably benign	Het
Tsbp1	C	A	17: 34,659,856 (GRCm39)	T93N	possibly damaging	Het
Zfp658	T	A	7: 43,223,413 (GRCm39)	S563T	probably benign	Het
Zswim9	G	A	7: 12,993,679 (GRCm39)	R826C	probably damaging	Het

Other mutations in Smarcd3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02401:Smarcd3	APN	5	24,798,717 (GRCm39)	missense	probably damaging	1.00
R0135:Smarcd3	UTSW	5	24,800,497 (GRCm39)	unclassified	probably benign
R1614:Smarcd3	UTSW	5	24,799,874 (GRCm39)	missense	possibly damaging	0.93
R1617:Smarcd3	UTSW	5	24,800,192 (GRCm39)	missense	probably damaging	1.00
R1753:Smarcd3	UTSW	5	24,800,820 (GRCm39)	nonsense	probably null
R1879:Smarcd3	UTSW	5	24,798,019 (GRCm39)	missense	probably damaging	0.99
R2307:Smarcd3	UTSW	5	24,800,746 (GRCm39)	missense	probably damaging	1.00
R3800:Smarcd3	UTSW	5	24,798,225 (GRCm39)	nonsense	probably null
R4592:Smarcd3	UTSW	5	24,797,802 (GRCm39)	missense	probably benign	0.00
R6369:Smarcd3	UTSW	5	24,799,982 (GRCm39)	missense	probably damaging	0.99
R6388:Smarcd3	UTSW	5	24,801,024 (GRCm39)	missense	possibly damaging	0.94
R7078:Smarcd3	UTSW	5	24,798,067 (GRCm39)	missense	probably damaging	0.98
R7341:Smarcd3	UTSW	5	24,800,435 (GRCm39)	missense	possibly damaging	0.95
R7426:Smarcd3	UTSW	5	24,800,810 (GRCm39)	missense	probably benign	0.30
R7806:Smarcd3	UTSW	5	24,798,260 (GRCm39)	missense	probably benign	0.45
R7935:Smarcd3	UTSW	5	24,801,024 (GRCm39)	missense	probably damaging	0.98
R8685:Smarcd3	UTSW	5	24,800,988 (GRCm39)	missense	probably damaging	1.00
R8769:Smarcd3	UTSW	5	24,803,792 (GRCm39)	missense	probably benign
R8877:Smarcd3	UTSW	5	24,798,990 (GRCm39)	missense	possibly damaging	0.93
R8984:Smarcd3	UTSW	5	24,798,986 (GRCm39)	missense	probably null	0.99
R9240:Smarcd3	UTSW	5	24,801,831 (GRCm39)	missense	probably benign	0.21
RF007:Smarcd3	UTSW	5	24,801,068 (GRCm39)	missense	probably damaging	0.98

Predicted Primers

PCR Primer
(F):5'- GAGGAGACAGCTACCTTTGGAG -3'
(R):5'- CTGCTCCTGATGCTGGACTATC -3'

Sequencing Primer
(F):5'- GGTGCTTCTGCTCCTCAGG -3'
(R):5'- GGACTATCAGGTTGGTTTTACCCC -3'

Posted On

2019-05-15