Mutagenetix > Incidental Mutation

Incidental Mutation 'R1531:Smarcd1'

166248

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

039570-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.874) question?

Stock #

R1531 (G1)

Quality Score

179

Status

Not validated

Chromosome

Chromosomal Location

99600175-99611872 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 99605264 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Serine at position 282 (C282S)

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

probably damaging
Transcript: ENSMUST00000023759
AA Change: C282S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000023759
Gene: ENSMUSG00000023018
AA Change: C282S

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: C241S

PolyPhen 2 Score 0.930 (Sensitivity: 0.81; Specificity: 0.94)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000229686

Predicted Effect

probably benign
Transcript: ENSMUST00000229845

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000229968

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000230748

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000230504

Predicted Effect

probably benign
Transcript: ENSMUST00000230530

Coding Region Coverage

1x: 99.0%
3x: 98.1%
10x: 95.6%
20x: 90.3%

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, 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: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Agtpbp1	T	A	13: 59,648,448 (GRCm39)		probably null	Het
Aldh3b2	T	G	19: 4,027,543 (GRCm39)	F28C	probably damaging	Het
Apaf1	T	C	10: 90,890,383 (GRCm39)	N540S	probably damaging	Het
Apob	T	C	12: 8,047,880 (GRCm39)	I953T	possibly damaging	Het
Arhgef1	A	G	7: 24,624,423 (GRCm39)	T816A	probably damaging	Het
Arid4a	T	A	12: 71,122,779 (GRCm39)	F1053L	probably benign	Het
Atxn1l	A	C	8: 110,458,691 (GRCm39)	F524V	probably damaging	Het
Cad	T	A	5: 31,233,563 (GRCm39)	M1874K	probably benign	Het
Ccdc40	G	A	11: 119,154,015 (GRCm39)	V1096I	probably benign	Het
Ccdc93	A	G	1: 121,408,551 (GRCm39)	D358G	probably benign	Het
Cd96	T	C	16: 45,938,169 (GRCm39)	T99A	probably benign	Het
Cdc42ep3	A	T	17: 79,642,473 (GRCm39)	M149K	probably benign	Het
Cgas	A	G	9: 78,349,763 (GRCm39)	Y200H	probably damaging	Het
Cog4	A	G	8: 111,606,353 (GRCm39)	E613G	probably benign	Het
Crebbp	A	T	16: 3,902,381 (GRCm39)	I2286N	probably benign	Het
Csf1	T	C	3: 107,655,654 (GRCm39)	E459G	possibly damaging	Het
Csrp2	A	T	10: 110,771,066 (GRCm39)	Y57F	probably benign	Het
Ctdspl	C	T	9: 118,869,650 (GRCm39)	P244L	probably damaging	Het
Cyp2c29	A	G	19: 39,313,412 (GRCm39)	R303G	probably damaging	Het
Cyp4a10	C	A	4: 115,375,632 (GRCm39)	Y38*	probably null	Het
Dmgdh	T	A	13: 93,880,919 (GRCm39)	I783N	probably damaging	Het
Efcc1	G	A	6: 87,708,148 (GRCm39)	E92K	probably benign	Het
Eif2ak4	T	A	2: 118,273,691 (GRCm39)	L872H	probably damaging	Het
Elp2	T	A	18: 24,764,461 (GRCm39)	S603T	probably benign	Het
Eml2	T	A	7: 18,930,179 (GRCm39)	L300H	probably damaging	Het
Esp3	A	G	17: 40,946,827 (GRCm39)	K50R	possibly damaging	Het
Esrp1	A	G	4: 11,379,375 (GRCm39)	F136L	probably damaging	Het
Exoc1	T	A	5: 76,707,011 (GRCm39)	D497E	probably damaging	Het
Fat3	A	G	9: 15,908,761 (GRCm39)	S2414P	probably damaging	Het
Foxj3	C	T	4: 119,477,398 (GRCm39)	P369S	unknown	Het
Gkn2	G	T	6: 87,352,921 (GRCm39)		probably null	Het
Gm17333	AAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAA	AAGAAGAGAAGAGAAGAGAAGAGAAGAGAA	16: 77,649,766 (GRCm39)		noncoding transcript	Het
Gm21905	A	T	5: 68,103,724 (GRCm39)		probably benign	Het
Grhl1	T	A	12: 24,632,962 (GRCm39)		probably null	Het
Grk6	A	G	13: 55,599,967 (GRCm39)	Y221C	probably damaging	Het
Hcrtr1	T	A	4: 130,024,720 (GRCm39)	K389*	probably null	Het
Hk1	G	A	10: 62,120,563 (GRCm39)	R545C	probably damaging	Het
Hsp90b1	A	T	10: 86,532,659 (GRCm39)	I339N	probably benign	Het
Ikzf3	T	C	11: 98,381,272 (GRCm39)	R103G	probably damaging	Het
Itgad	A	C	7: 127,777,542 (GRCm39)	I141L	probably benign	Het
Jmjd6	T	A	11: 116,733,266 (GRCm39)	Y137F	probably benign	Het
Kcna1	A	G	6: 126,619,030 (GRCm39)	V430A	probably benign	Het
Kel	A	G	6: 41,665,560 (GRCm39)	V520A	probably damaging	Het
Klhl41	G	A	2: 69,501,084 (GRCm39)	V182I	probably benign	Het
Ldhb	C	A	6: 142,447,121 (GRCm39)	M64I	probably benign	Het
Lrrc23	A	G	6: 124,753,077 (GRCm39)	S190P	possibly damaging	Het
Mboat2	T	C	12: 25,009,029 (GRCm39)	V445A	probably benign	Het
Mlycd	G	A	8: 120,128,258 (GRCm39)	W188*	probably null	Het
Mpp3	C	T	11: 101,899,475 (GRCm39)	E349K	probably benign	Het
Mtres1	A	G	10: 43,401,316 (GRCm39)	V211A	probably benign	Het
Myh4	A	G	11: 67,141,366 (GRCm39)	M780V	probably benign	Het
Myh6	G	A	14: 55,193,963 (GRCm39)	R809C	probably damaging	Het
Mylip	G	A	13: 45,560,046 (GRCm39)	V161M	possibly damaging	Het
Nrp1	G	A	8: 129,152,450 (GRCm39)	V220I	probably null	Het
Nup210	A	T	6: 91,011,823 (GRCm39)	N455K	probably benign	Het
Or14j10	A	T	17: 37,935,243 (GRCm39)	Y94*	probably null	Het
Or51f1d	C	A	7: 102,700,795 (GRCm39)	Q97K	probably benign	Het
Pbld2	G	T	10: 62,889,732 (GRCm39)		probably null	Het
Pclo	C	G	5: 14,571,917 (GRCm39)	P434R	probably damaging	Het
Pdlim3	A	G	8: 46,349,800 (GRCm39)	K37E	probably damaging	Het
Prkdc	T	A	16: 15,589,970 (GRCm39)	I2611N	probably benign	Het
Prr12	T	C	7: 44,677,954 (GRCm39)	D2019G	unknown	Het
Rab27a	A	G	9: 73,002,685 (GRCm39)	T205A	probably benign	Het
Rcan3	A	G	4: 135,152,595 (GRCm39)	L42P	probably damaging	Het
Rchy1	T	C	5: 92,103,474 (GRCm39)		probably null	Het
Sema6a	T	C	18: 47,382,066 (GRCm39)	H827R	probably damaging	Het
Sertad4	A	G	1: 192,533,258 (GRCm39)		probably null	Het
Speg	A	G	1: 75,377,866 (GRCm39)	T769A	possibly damaging	Het
Syne1	T	A	10: 5,297,875 (GRCm39)	K1141*	probably null	Het
Synpo2	T	C	3: 122,911,315 (GRCm39)	E110G	probably benign	Het
Tg	T	A	15: 66,722,351 (GRCm39)	D333E	probably benign	Het
Tmem132c	A	G	5: 127,436,955 (GRCm39)	Y148C	probably damaging	Het
Tmem215	T	A	4: 40,473,965 (GRCm39)	V14E	probably damaging	Het
Tmem229b	A	G	12: 79,011,685 (GRCm39)	L82P	probably damaging	Het
Togaram1	A	G	12: 65,013,039 (GRCm39)	T97A	probably benign	Het
Trappc9	G	A	15: 72,565,397 (GRCm39)	R965*	probably null	Het
Trio	T	C	15: 27,833,071 (GRCm39)	I104V	probably benign	Het
Trp73	A	G	4: 154,148,352 (GRCm39)	F354S	probably benign	Het
Ttyh2	T	C	11: 114,577,278 (GRCm39)	L63P	probably damaging	Het
Ulk4	G	C	9: 120,873,841 (GRCm39)	P1197A	probably damaging	Het
Vmn1r176	T	C	7: 23,534,536 (GRCm39)	M206V	possibly damaging	Het
Vps8	T	A	16: 21,285,226 (GRCm39)	Y402*	probably null	Het
Zbtb41	A	G	1: 139,350,931 (GRCm39)	I15V	probably benign	Het
Zc3hav1	T	C	6: 38,284,170 (GRCm39)	I982V	possibly damaging	Het
Zmynd19	T	A	2: 24,848,123 (GRCm39)	N106K	probably benign	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
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
R6450:Smarcd1	UTSW	15	99,605,766 (GRCm39)	missense	possibly damaging	0.85
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'- ATGTTCTCGTAGGGAGGTCGTCAC -3'
(R):5'- GGCGCTCAGTACAGGAACACATTC -3'

Sequencing Primer
(F):5'- atccacctgcctctgcc -3'
(R):5'- CAATCTAACAAACATTGGCAAATCTG -3'

Posted On

2014-04-13