Mutagenetix > Incidental Mutation

Incidental Mutation 'R0522:Spg20'

48615

Institutional Source

Beutler Lab

Gene Symbol

Spg20

Ensembl Gene

ENSMUSG00000036580

Gene Name

spastic paraplegia 20, spartin (Troyer syndrome) homolog (human)

Synonyms

TAHCCP1

MMRRC Submission

038715-MU

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.232) question?

Stock #

R0522 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

55112108-55137322 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 55128365 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Arginine at position 548 (S548R)

Ref Sequence

ENSEMBL: ENSMUSP00000113621 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000044116] [ENSMUST00000107971] [ENSMUST00000117341] [ENSMUST00000118118]

AlphaFold

Q8R1X6

Predicted Effect

probably damaging
Transcript: ENSMUST00000044116
AA Change: S548R

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

SMART Domains

Protein: ENSMUSP00000042367
Gene: ENSMUSG00000036580
AA Change: S548R

Domain	Start	End	E-Value	Type
MIT	16	94	4.64e-18	SMART
SCOP:d1bw0a_	158	254	8e-4	SMART
low complexity region	369	381	N/A	INTRINSIC
low complexity region	408	426	N/A	INTRINSIC
Pfam:Senescence	431	616	9.7e-52	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000107971
AA Change: S491R

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

SMART Domains

Protein: ENSMUSP00000103605
Gene: ENSMUSG00000036580
AA Change: S491R

Domain	Start	End	E-Value	Type
MIT	16	94	4.64e-18	SMART
SCOP:d1bw0a_	158	254	9e-4	SMART
low complexity region	351	369	N/A	INTRINSIC
Pfam:Senescence	373	560	3.2e-56	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000117341
AA Change: S548R

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

SMART Domains

Protein: ENSMUSP00000113968
Gene: ENSMUSG00000036580
AA Change: S548R

Domain	Start	End	E-Value	Type
MIT	16	94	4.64e-18	SMART
SCOP:d1bw0a_	158	254	8e-4	SMART
low complexity region	369	381	N/A	INTRINSIC
low complexity region	408	426	N/A	INTRINSIC
Pfam:Senescence	430	582	9.3e-42	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000118118
AA Change: S548R

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

SMART Domains

Protein: ENSMUSP00000113621
Gene: ENSMUSG00000036580
AA Change: S548R

Domain	Start	End	E-Value	Type
MIT	16	94	4.64e-18	SMART
SCOP:d1bw0a_	158	254	8e-4	SMART
low complexity region	369	381	N/A	INTRINSIC
low complexity region	408	426	N/A	INTRINSIC
Pfam:Senescence	430	617	3.8e-56	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000199416

Meta Mutation Damage Score

0.1421

Coding Region Coverage

1x: 99.1%
3x: 98.2%
10x: 95.8%
20x: 90.8%

Validation Efficiency

100% (67/67)

MGI Phenotype

PHENOTYPE: Mice homozygous for a knock-out allele exhibit impaired lipid droplet amintenance, cytokinesis and impaired motor coordination. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9130409I23Rik	A	C	1: 181,059,747	D299A	probably damaging	Het
Adgre5	A	G	8: 83,730,176	I192T	probably benign	Het
Adgrl3	T	C	5: 81,726,801	Y982H	possibly damaging	Het
Adgrv1	T	A	13: 81,528,442		probably benign	Het
Alms1	T	C	6: 85,621,615	V1610A	probably benign	Het
Ankrd24	T	C	10: 81,636,355		probably benign	Het
C2cd3	A	G	7: 100,395,222	N337S	probably benign	Het
Cdc40	T	C	10: 40,857,612	Y114C	probably benign	Het
Cdhr1	A	T	14: 37,094,000		probably null	Het
Cfc1	G	A	1: 34,537,153	C98Y	probably damaging	Het
Cyp11b2	A	T	15: 74,851,684		probably benign	Het
Cyth4	C	A	15: 78,615,785	H255Q	possibly damaging	Het
Dip2a	T	C	10: 76,321,531	K80R	probably benign	Het
Dnajb5	G	T	4: 42,957,083	D257Y	probably damaging	Het
Dynll1	T	C	5: 115,300,506		probably benign	Het
Edn1	T	A	13: 42,304,954	V81E	probably damaging	Het
F5	T	C	1: 164,211,763	S1981P	probably damaging	Het
Fam186b	T	A	15: 99,280,519	M309L	probably benign	Het
Gm14221	G	A	2: 160,574,677		noncoding transcript	Het
Gnptab	T	A	10: 88,431,466		probably benign	Het
Golgb1	AAGAGAGAGAGAGAGA	AAGAGAGAGAGAGA	16: 36,915,205		probably null	Het
Gpr176	A	G	2: 118,284,012	C106R	probably damaging	Het
Hdac7	A	T	15: 97,806,679		probably null	Het
Hlx	T	C	1: 184,731,640	S168G	probably damaging	Het
Hnf1a	G	T	5: 114,950,688		probably benign	Het
Hp1bp3	C	T	4: 138,222,161	L19F	possibly damaging	Het
Hspa14	T	A	2: 3,511,049	T63S	probably damaging	Het
Insrr	C	T	3: 87,800,872	S207F	probably damaging	Het
Jak3	C	A	8: 71,682,274		probably benign	Het
Jmjd7	G	A	2: 120,030,341	A91T	probably damaging	Het
Lgals9	G	T	11: 78,965,812	H265Q	possibly damaging	Het
Lrriq1	T	G	10: 103,161,777	N1326H	probably damaging	Het
Mdn1	C	A	4: 32,672,837	Q486K	probably benign	Het
Mpeg1	A	G	19: 12,461,759	T194A	probably damaging	Het
Nek5	T	A	8: 22,088,797		probably benign	Het
Pcgf2	A	C	11: 97,692,047	I135M	probably benign	Het
Phactr1	G	T	13: 43,059,591	A222S	probably benign	Het
Pla2r1	T	C	2: 60,479,515	S575G	probably benign	Het
Plcg2	T	C	8: 117,614,288		probably null	Het
Pold3	A	G	7: 100,121,383	V14A	probably damaging	Het
Polg	A	G	7: 79,460,151		probably benign	Het
Poteg	T	G	8: 27,449,958	L48V	possibly damaging	Het
Prmt1	A	T	7: 44,981,779	C50S	probably benign	Het
Prx	T	A	7: 27,518,195	V707E	probably damaging	Het
Rrp12	C	T	19: 41,874,705		probably benign	Het
Saxo1	A	T	4: 86,445,103	V381E	probably damaging	Het
Sh2d2a	T	C	3: 87,847,109		probably null	Het
Slc26a5	A	C	5: 21,846,345	I57R	probably damaging	Het
Slc38a3	T	A	9: 107,655,213		probably null	Het
Slc5a4b	T	C	10: 76,090,700	T188A	probably damaging	Het
Slc7a13	A	G	4: 19,824,010	I260V	probably benign	Het
Smg8	A	T	11: 87,086,462	S98T	probably benign	Het
Sult6b1	C	T	17: 78,905,529	G98S	probably damaging	Het
Tbc1d2	A	G	4: 46,649,806	Y77H	probably damaging	Het
Tet2	T	A	3: 133,466,804	D1899V	probably damaging	Het
Tmcc1	C	CAT	6: 116,042,870		probably null	Het
Tnfrsf21	C	T	17: 43,038,213	H239Y	probably benign	Het
Trp53bp1	C	A	2: 121,251,868	A317S	probably null	Het
Uap1l1	T	C	2: 25,363,277	E382G	probably damaging	Het
Ugt1a10	C	T	1: 88,218,249	P473L	probably damaging	Het
Ugt1a9	T	C	1: 88,071,392	V188A	probably damaging	Het
Virma	T	C	4: 11,519,416		probably null	Het
Xrcc6	T	C	15: 82,022,592		probably benign	Het
Zfp719	A	G	7: 43,589,253		probably null	Het
Zfp804b	T	A	5: 6,772,014	T350S	probably benign	Het
Zfp959	G	T	17: 55,896,201	R61M	probably null	Het

Other mutations in Spg20

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01160:Spg20	APN	3	55121756	missense	probably damaging	1.00
IGL01539:Spg20	APN	3	55117302	missense	possibly damaging	0.95
IGL01982:Spg20	APN	3	55128490	splice site	probably null
IGL02345:Spg20	APN	3	55117726	splice site	probably null
IGL03217:Spg20	APN	3	55128491	splice site	probably benign
IGL03344:Spg20	APN	3	55121685	missense	probably benign	0.03
BB007:Spg20	UTSW	3	55128276	missense	probably damaging	1.00
BB017:Spg20	UTSW	3	55128276	missense	probably damaging	1.00
R0145:Spg20	UTSW	3	55127671	nonsense	probably null
R1506:Spg20	UTSW	3	55117571	missense	probably damaging	0.99
R2043:Spg20	UTSW	3	55127548	missense	probably damaging	1.00
R2183:Spg20	UTSW	3	55117133	missense	probably benign	0.43
R4022:Spg20	UTSW	3	55117736	missense	probably damaging	1.00
R5154:Spg20	UTSW	3	55117329	missense	probably damaging	1.00
R5869:Spg20	UTSW	3	55135510	missense	probably benign	0.00
R5987:Spg20	UTSW	3	55126541	missense	probably benign	0.00
R6142:Spg20	UTSW	3	55117248	missense	probably damaging	1.00
R6185:Spg20	UTSW	3	55117219	missense	probably damaging	1.00
R6652:Spg20	UTSW	3	55124827	missense	probably benign	0.00
R6791:Spg20	UTSW	3	55127561	missense	probably damaging	1.00
R7131:Spg20	UTSW	3	55121799	critical splice donor site	probably null
R7930:Spg20	UTSW	3	55128276	missense	probably damaging	1.00
R8005:Spg20	UTSW	3	55117352	missense	probably benign	0.00
R8458:Spg20	UTSW	3	55124894	missense	probably damaging	1.00
R8734:Spg20	UTSW	3	55124879	missense	possibly damaging	0.92
R8791:Spg20	UTSW	3	55121679	missense	probably benign	0.19
R8929:Spg20	UTSW	3	55128558	missense	possibly damaging	0.96
R9060:Spg20	UTSW	3	55124854	missense	probably benign	0.02
R9172:Spg20	UTSW	3	55124846	missense	possibly damaging	0.68
R9539:Spg20	UTSW	3	55127503	missense	probably damaging	1.00
R9695:Spg20	UTSW	3	55126534	missense	probably benign
RF009:Spg20	UTSW	3	55127606	missense	probably benign	0.00
X0018:Spg20	UTSW	3	55135499	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GTTCACCTAGCAGGCACAGTAACAC -3'
(R):5'- CCCTTGCCAGACAGTTGAGAATCC -3'

Sequencing Primer
(F):5'- CCATGCCAGAAACGGGTTG -3'
(R):5'- CAGACAGTTGAGAATCCTGTAAAC -3'

Posted On

2013-06-12