Mutagenetix > Incidental Mutation

Incidental Mutation 'R1775:Samhd1'

204294

Institutional Source

Beutler Lab

Gene Symbol

Samhd1

Ensembl Gene

ENSMUSG00000027639

Gene Name

SAM domain and HD domain, 1

Synonyms

E330031J07Rik

MMRRC Submission

039806-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1775 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

156939454-156977016 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 156949467 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 473 (V473A)

Ref Sequence

ENSEMBL: ENSMUSP00000105176 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000057725] [ENSMUST00000088523] [ENSMUST00000109549] [ENSMUST00000123932]

AlphaFold

Q60710

Predicted Effect

probably benign
Transcript: ENSMUST00000057725
AA Change: V473A

PolyPhen 2 Score 0.095 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000059717
Gene: ENSMUSG00000027639
AA Change: V473A

Domain	Start	End	E-Value	Type
low complexity region	49	65	N/A	INTRINSIC
SAM	74	142	4.4e-14	SMART
HDc	192	357	1.89e-9	SMART
Blast:HDc	398	437	1e-16	BLAST
low complexity region	506	517	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000088523
AA Change: V473A

PolyPhen 2 Score 0.095 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000085880
Gene: ENSMUSG00000027639
AA Change: V473A

Domain	Start	End	E-Value	Type
low complexity region	49	65	N/A	INTRINSIC
SAM	74	142	4.4e-14	SMART
HDc	192	357	1.89e-9	SMART
Blast:HDc	398	437	2e-16	BLAST
low complexity region	506	517	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000109549
AA Change: V473A

PolyPhen 2 Score 0.158 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000105176
Gene: ENSMUSG00000027639
AA Change: V473A

Domain	Start	End	E-Value	Type
low complexity region	49	65	N/A	INTRINSIC
SAM	74	142	4.4e-14	SMART
HDc	192	357	1.89e-9	SMART
Blast:HDc	398	437	1e-16	BLAST
low complexity region	506	517	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000123932

SMART Domains

Protein: ENSMUSP00000124599
Gene: ENSMUSG00000027639

Domain	Start	End	E-Value	Type
low complexity region	18	34	N/A	INTRINSIC
SAM	43	112	1.51e-3	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139149

Predicted Effect

unknown
Transcript: ENSMUST00000139263
AA Change: V452A

SMART Domains

Protein: ENSMUSP00000124935
Gene: ENSMUSG00000027639
AA Change: V452A

Domain	Start	End	E-Value	Type
low complexity region	29	45	N/A	INTRINSIC
SAM	54	122	4.4e-14	SMART
HDc	172	337	1.89e-9	SMART
Blast:HDc	378	417	2e-16	BLAST
low complexity region	486	497	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142508

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160213

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.5%
20x: 92.9%

Validation Efficiency

98% (95/97)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene may play a role in regulation of the innate immune response. The encoded protein is upregulated in response to viral infection and may be involved in mediation of tumor necrosis factor-alpha proinflammatory responses. Mutations in this gene have been associated with Aicardi-Goutieres syndrome. [provided by RefSeq, Mar 2010]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit increased susceptibility to infection with pseudotyped HIV-1. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700034J04Rik	A	G	12: 11,272,143 (GRCm39)	S20P	unknown	Het
4921528I07Rik	G	A	9: 114,108,386 (GRCm39)		noncoding transcript	Het
4930562C15Rik	G	A	16: 4,669,422 (GRCm39)		probably null	Het
4933427I04Rik	A	G	4: 123,754,286 (GRCm39)	T67A	possibly damaging	Het
Abcc2	A	T	19: 43,786,858 (GRCm39)	N160Y	possibly damaging	Het
Acaca	A	G	11: 84,191,248 (GRCm39)	D155G	possibly damaging	Het
Afg3l1	G	A	8: 124,219,639 (GRCm39)	R389Q	possibly damaging	Het
Ank2	G	A	3: 126,728,196 (GRCm39)	T799M	probably benign	Het
Anxa2	T	C	9: 69,395,363 (GRCm39)	Y202H	possibly damaging	Het
Arhgef33	A	G	17: 80,681,172 (GRCm39)	T771A	probably benign	Het
Atp12a	T	C	14: 56,610,046 (GRCm39)	V182A	probably benign	Het
Birc6	T	C	17: 74,919,281 (GRCm39)	L210S	probably damaging	Het
Car3	A	G	3: 14,929,492 (GRCm39)	T73A	probably benign	Het
Cd5l	T	C	3: 87,275,966 (GRCm39)	L312P	probably damaging	Het
Celf5	A	G	10: 81,303,138 (GRCm39)		probably benign	Het
Cep290	T	A	10: 100,332,672 (GRCm39)	V257E	probably damaging	Het
Cntrob	T	C	11: 69,211,693 (GRCm39)	D177G	possibly damaging	Het
Copg2	A	T	6: 30,787,271 (GRCm39)	F658I	probably damaging	Het
Csmd3	T	C	15: 47,763,135 (GRCm39)	T1234A	probably damaging	Het
Dhx35	A	G	2: 158,648,357 (GRCm39)	T72A	probably damaging	Het
Dmrtc2	A	T	7: 24,573,792 (GRCm39)	H209L	possibly damaging	Het
Eml5	G	T	12: 98,818,963 (GRCm39)		probably null	Het
Evpl	T	C	11: 116,114,486 (GRCm39)	E1068G	possibly damaging	Het
Ezh2	A	G	6: 47,553,594 (GRCm39)	M41T	probably damaging	Het
Fmo3	A	G	1: 162,796,294 (GRCm39)	S93P	possibly damaging	Het
Gdi2	A	G	13: 3,610,018 (GRCm39)	Y213C	possibly damaging	Het
Gpr15	A	T	16: 58,538,921 (GRCm39)	I56K	probably benign	Het
Gria2	G	T	3: 80,598,645 (GRCm39)	S796R	probably benign	Het
Hectd4	T	A	5: 121,429,254 (GRCm39)		probably benign	Het
Hgfac	T	C	5: 35,200,194 (GRCm39)		probably benign	Het
Hspg2	C	T	4: 137,247,467 (GRCm39)	R1200W	probably damaging	Het
Ift52	G	A	2: 162,867,275 (GRCm39)	D78N	possibly damaging	Het
Iqca1	C	A	1: 90,009,138 (GRCm39)	W415L	probably damaging	Het
Ism1	A	T	2: 139,587,963 (GRCm39)	K236N	probably damaging	Het
Itgb6	C	T	2: 60,502,988 (GRCm39)	W43*	probably null	Het
Kcnk18	T	A	19: 59,223,773 (GRCm39)	I306N	probably damaging	Het
Kctd8	T	C	5: 69,497,903 (GRCm39)	K248E	probably damaging	Het
Layn	T	A	9: 50,970,833 (GRCm39)	I237F	probably benign	Het
Lce3f	C	T	3: 92,900,248 (GRCm39)	P23L	unknown	Het
Lct	A	G	1: 128,228,038 (GRCm39)	F1152L	probably damaging	Het
Mettl25b	A	G	3: 87,831,124 (GRCm39)	S404P	probably damaging	Het
Mxra8	T	C	4: 155,927,531 (GRCm39)	I413T	probably damaging	Het
Nedd9	A	G	13: 41,471,438 (GRCm39)	V187A	probably benign	Het
Net1	A	G	13: 3,937,642 (GRCm39)	L207P	probably damaging	Het
Neurod1	G	T	2: 79,284,781 (GRCm39)	P201T	probably benign	Het
Nlrp1b	A	G	11: 71,052,647 (GRCm39)	F927S	probably damaging	Het
Ntrk3	T	A	7: 78,005,789 (GRCm39)	H524L	possibly damaging	Het
Nup98	A	C	7: 101,784,144 (GRCm39)	S1063A	probably benign	Het
Or10ak11	T	A	4: 118,687,065 (GRCm39)	M191L	probably benign	Het
Or11h4b	G	T	14: 50,918,623 (GRCm39)	P156Q	possibly damaging	Het
Or56b1	G	A	7: 104,285,366 (GRCm39)	V162I	probably benign	Het
Or5b97	C	A	19: 12,878,599 (GRCm39)	V182F	probably benign	Het
Or5m9b	G	A	2: 85,905,104 (GRCm39)	V7I	possibly damaging	Het
Or6d15	T	C	6: 116,559,925 (GRCm39)		probably benign	Het
Pdzd2	G	A	15: 12,592,546 (GRCm39)	R33W	probably damaging	Het
Phf21a	G	A	2: 92,160,860 (GRCm39)	V243I	probably damaging	Het
Ppp1r12b	A	G	1: 134,821,086 (GRCm39)		probably null	Het
Rexo5	T	C	7: 119,444,634 (GRCm39)	V703A	probably benign	Het
Rgs4	A	G	1: 169,572,847 (GRCm39)	S30P	probably benign	Het
Rxra	C	A	2: 27,646,256 (GRCm39)	D340E	probably damaging	Het
Scn3a	T	A	2: 65,302,686 (GRCm39)	K1253N	probably damaging	Het
Scn7a	T	C	2: 66,511,299 (GRCm39)	N1207S	probably benign	Het
Sec24d	T	A	3: 123,130,166 (GRCm39)	I443N	probably damaging	Het
Sema4g	T	A	19: 44,987,681 (GRCm39)		probably null	Het
Sema5b	A	G	16: 35,480,694 (GRCm39)	K787R	probably benign	Het
Serpinc1	A	G	1: 160,817,217 (GRCm39)	N104D	probably benign	Het
Sfn	T	C	4: 133,328,542 (GRCm39)	H180R	probably damaging	Het
Slc22a6	G	T	19: 8,596,471 (GRCm39)		probably null	Het
Slc9a8	T	C	2: 167,299,278 (GRCm39)	S217P	probably benign	Het
Smc6	A	G	12: 11,359,270 (GRCm39)	N965D	probably benign	Het
Sod2	T	A	17: 13,233,919 (GRCm39)	I177N	probably damaging	Het
Sp4	A	T	12: 118,263,335 (GRCm39)	I237K	probably damaging	Het
Sulf2	T	C	2: 165,921,532 (GRCm39)	K697R	probably benign	Het
Svs4	A	T	2: 164,119,005 (GRCm39)	D110E	unknown	Het
Tas1r1	T	A	4: 152,122,675 (GRCm39)	R57*	probably null	Het
Tlr5	T	C	1: 182,801,287 (GRCm39)	I197T	probably damaging	Het
Tmc3	T	C	7: 83,261,740 (GRCm39)	V606A	probably benign	Het
Tmem241	T	A	18: 12,251,469 (GRCm39)	L37F	probably damaging	Het
Tmem59l	A	T	8: 70,938,903 (GRCm39)	N90K	probably damaging	Het
Tram1	A	C	1: 13,646,680 (GRCm39)		probably benign	Het
Trim15	T	A	17: 37,176,061 (GRCm39)	H162L	probably benign	Het
Ttc28	T	A	5: 111,424,677 (GRCm39)	Y1501N	probably benign	Het
Ttc34	T	C	4: 154,946,671 (GRCm39)	V857A	probably benign	Het
Tulp4	A	G	17: 6,189,321 (GRCm39)	T48A	probably damaging	Het
Usp9y	T	C	Y: 1,368,089 (GRCm39)	E939G	probably damaging	Het
Utp20	A	G	10: 88,606,670 (GRCm39)	I1634T	probably benign	Het
Vmn2r72	T	C	7: 85,387,378 (GRCm39)	M729V	probably benign	Het
Vps13c	C	T	9: 67,788,729 (GRCm39)	T334M	probably damaging	Het
Wnk4	C	G	11: 101,167,166 (GRCm39)		probably benign	Het
Xpo1	A	G	11: 23,221,193 (GRCm39)	N97D	probably benign	Het
Xpo4	A	T	14: 57,841,129 (GRCm39)	F518Y	probably benign	Het
Zfp668	C	T	7: 127,465,778 (GRCm39)	V469I	possibly damaging	Het
Zfp85	C	A	13: 67,897,823 (GRCm39)	C83F	probably damaging	Het

Other mutations in Samhd1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00792:Samhd1	APN	2	156,962,468 (GRCm39)	missense	probably damaging	1.00
IGL00903:Samhd1	APN	2	156,949,343 (GRCm39)	splice site	probably benign
IGL01313:Samhd1	APN	2	156,958,321 (GRCm39)	missense	probably damaging	1.00
IGL01775:Samhd1	APN	2	156,956,250 (GRCm39)	splice site	probably benign
IGL02245:Samhd1	APN	2	156,952,475 (GRCm39)	missense	possibly damaging	0.46
IGL02314:Samhd1	APN	2	156,976,948 (GRCm39)	missense	probably damaging	0.98
R0390:Samhd1	UTSW	2	156,956,151 (GRCm39)	missense	probably damaging	1.00
R0487:Samhd1	UTSW	2	156,952,535 (GRCm39)	missense	probably damaging	1.00
R0842:Samhd1	UTSW	2	156,965,251 (GRCm39)	missense	probably damaging	0.99
R1199:Samhd1	UTSW	2	156,951,381 (GRCm39)	missense	probably damaging	0.99
R1681:Samhd1	UTSW	2	156,943,652 (GRCm39)	missense	probably benign	0.45
R2859:Samhd1	UTSW	2	156,948,149 (GRCm39)	critical splice donor site	probably null
R2903:Samhd1	UTSW	2	156,965,335 (GRCm39)	missense	possibly damaging	0.95
R2905:Samhd1	UTSW	2	156,965,335 (GRCm39)	missense	possibly damaging	0.95
R3983:Samhd1	UTSW	2	156,965,369 (GRCm39)	missense	possibly damaging	0.81
R4432:Samhd1	UTSW	2	156,946,813 (GRCm39)	missense	probably damaging	0.99
R4576:Samhd1	UTSW	2	156,943,670 (GRCm39)	missense	probably damaging	1.00
R5283:Samhd1	UTSW	2	156,951,412 (GRCm39)	missense	possibly damaging	0.70
R5741:Samhd1	UTSW	2	156,954,751 (GRCm39)	missense	probably benign
R6021:Samhd1	UTSW	2	156,962,474 (GRCm39)	critical splice acceptor site	probably null
R6518:Samhd1	UTSW	2	156,956,217 (GRCm39)	missense	possibly damaging	0.62
R6818:Samhd1	UTSW	2	156,949,417 (GRCm39)	missense	probably benign	0.04
R6924:Samhd1	UTSW	2	156,951,403 (GRCm39)	missense	probably benign	0.00
R7307:Samhd1	UTSW	2	156,976,940 (GRCm39)	missense	probably benign	0.27
R7337:Samhd1	UTSW	2	156,948,164 (GRCm39)	missense	probably damaging	0.99
R7596:Samhd1	UTSW	2	156,943,754 (GRCm39)	missense	probably damaging	1.00
R7892:Samhd1	UTSW	2	156,958,415 (GRCm39)	missense	probably damaging	1.00
R8081:Samhd1	UTSW	2	156,943,358 (GRCm39)	nonsense	probably null
R8234:Samhd1	UTSW	2	156,958,270 (GRCm39)	critical splice donor site	probably null
R8400:Samhd1	UTSW	2	156,941,353 (GRCm39)	missense	probably benign	0.19
R8690:Samhd1	UTSW	2	156,971,794 (GRCm39)	missense	probably benign	0.00
R9090:Samhd1	UTSW	2	156,956,205 (GRCm39)	missense	probably damaging	1.00
R9271:Samhd1	UTSW	2	156,956,205 (GRCm39)	missense	probably damaging	1.00
R9765:Samhd1	UTSW	2	156,965,219 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGGCTTGCTCTTGAGAACAG -3'
(R):5'- ATCCGTTGGTTCCAATGCACTC -3'

Sequencing Primer
(F):5'- TGGGTCTCACCCAAATAC -3'
(R):5'- GGTTCCAATGCACTCTCAGTTC -3'

Posted On

2014-06-23