Mutagenetix > Incidental Mutations

Incidental Mutation 'R5869:Spg20'

454314

Institutional Source

Beutler Lab

Gene Symbol

Spg20

Ensembl Gene

ENSMUSG00000036580

Gene Name

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

Synonyms

TAHCCP1

MMRRC Submission

044077-MU

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.231) question?

Stock #

R5869 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

55112108-55137322 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 55135510 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Leucine at position 616 (M616L)

Ref Sequence

ENSEMBL: ENSMUSP00000113621 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000044116] [ENSMUST00000052904] [ENSMUST00000061099] [ENSMUST00000107971] [ENSMUST00000118118] [ENSMUST00000118963] [ENSMUST00000153009]

AlphaFold

Q8R1X6

Predicted Effect

probably benign
Transcript: ENSMUST00000044116
AA Change: M616L

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000042367
Gene: ENSMUSG00000036580
AA Change: M616L

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 benign
Transcript: ENSMUST00000052904

SMART Domains

Protein: ENSMUSP00000049698
Gene: ENSMUSG00000048655

Domain	Start	End	E-Value	Type
Pfam:DUF4600	1	100	2e-38	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000061099

SMART Domains

Protein: ENSMUSP00000054771
Gene: ENSMUSG00000048655

Domain	Start	End	E-Value	Type
Pfam:DUF4600	54	181	1.8e-58	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000107971
AA Change: M559L

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000103605
Gene: ENSMUSG00000036580
AA Change: M559L

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 benign
Transcript: ENSMUST00000118118
AA Change: M616L

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000113621
Gene: ENSMUSG00000036580
AA Change: M616L

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

probably benign
Transcript: ENSMUST00000118963

SMART Domains

Protein: ENSMUSP00000112414
Gene: ENSMUSG00000048655

Domain	Start	End	E-Value	Type
Pfam:DUF4600	53	182	1.2e-55	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000153009

Meta Mutation Damage Score

0.0622

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.5%
20x: 92.1%

Validation Efficiency

93% (68/73)

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: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adarb1	T	C	10: 77,325,616		probably benign	Het
Arsk	T	C	13: 76,091,784	E100G	probably benign	Het
Ascc3	C	T	10: 50,842,183	R1991*	probably null	Het
Aspscr1	T	C	11: 120,688,920	I31T	possibly damaging	Het
Asz1	T	C	6: 18,074,940		probably benign	Het
Calm5	T	A	13: 3,854,321		probably benign	Het
Car5a	G	A	8: 121,916,380	T295I	probably benign	Het
Ccdc174	T	A	6: 91,885,418		probably benign	Het
Celsr2	G	A	3: 108,413,909	A529V	probably damaging	Het
Cep192	A	G	18: 67,815,864	D252G	probably benign	Het
Clcnka	A	G	4: 141,394,965	F217L	probably benign	Het
Cnot3	A	T	7: 3,644,930		probably benign	Het
Coro1c	A	G	5: 113,850,846		probably benign	Het
Cstf3	A	G	2: 104,659,240		probably null	Het
Dcdc2a	C	T	13: 25,107,730	P233S	probably benign	Het
Ddx55	A	G	5: 124,568,682	T581A	probably benign	Het
Exo1	T	C	1: 175,901,283	S638P	possibly damaging	Het
Fam135a	T	C	1: 24,029,430	E616G	possibly damaging	Het
Fignl2	T	C	15: 101,053,280	S374G	unknown	Het
Gm4799	A	T	10: 82,954,449		noncoding transcript	Het
Hectd4	T	C	5: 121,343,225		probably null	Het
Ighv1-76	T	C	12: 115,848,038	E65G	probably damaging	Het
Igsf9b	C	A	9: 27,323,235	H465Q	probably benign	Het
Itga9	A	G	9: 118,663,889	D284G	probably damaging	Het
Itpr1	T	C	6: 108,473,529	S1940P	probably benign	Het
Kcnb1	A	G	2: 167,188,071	S185P	probably benign	Het
Kif20a	G	A	18: 34,632,415	A822T	probably benign	Het
Krt1	A	T	15: 101,850,131	F199L	probably damaging	Het
Lpin2	A	G	17: 71,232,276		probably benign	Het
Lrp1b	A	C	2: 41,004,603	D2204E	probably damaging	Het
Mier3	T	A	13: 111,714,850	N427K	probably damaging	Het
Mmp12	GTAATAATAATAATAATAAT	GTAATAATAATAATAAT	9: 7,348,446		probably benign	Het
Mroh3	T	A	1: 136,186,123	M643L	probably benign	Het
Myh11	A	G	16: 14,230,800	S548P	probably damaging	Het
Nat8f6	A	C	6: 85,808,523	L215V	possibly damaging	Het
Nlrp3	G	A	11: 59,548,134	R179Q	probably damaging	Het
Nup88	T	C	11: 70,969,671	E94G	probably benign	Het
Pias1	A	T	9: 62,912,766	D306E	probably benign	Het
Pick1	A	G	15: 79,248,895	D385G	probably benign	Het
Pitx3	A	T	19: 46,137,296		probably benign	Het
Plpp3	T	A	4: 105,194,962		probably null	Het
Prlhr	C	A	19: 60,467,621	R169L	probably damaging	Het
Ptprf	A	C	4: 118,210,382	M1872R	probably damaging	Het
Ptprh	T	C	7: 4,601,940	D35G	probably benign	Het
Rnf130	A	G	11: 50,085,815		probably null	Het
Rnf17	A	C	14: 56,505,988	E1337A	possibly damaging	Het
Sdk2	A	G	11: 113,851,882	Y734H	probably damaging	Het
Slc25a10	C	T	11: 120,498,117	T269I	probably damaging	Het
Slc4a11	A	C	2: 130,684,459	V855G	probably benign	Het
Slc5a5	C	A	8: 70,892,330	R111L	probably damaging	Het
Tmem229a	T	C	6: 24,954,687	D356G	probably damaging	Het
Tmem30c	A	G	16: 57,266,562	S293P	probably damaging	Het
Tnfrsf14	C	A	4: 154,926,598		probably null	Het
Tnfrsf19	C	T	14: 60,971,178	R298H	possibly damaging	Het
Ttc21a	A	G	9: 119,958,792	K809E	probably benign	Het
Ttn	G	A	2: 76,750,209	P23447S	probably damaging	Het
Uap1	T	A	1: 170,151,138		probably null	Het
Wdr82	A	G	9: 106,185,304	Q252R	probably benign	Het
Zfp523	T	C	17: 28,194,993	I34T	probably benign	Het
Zfp808	T	A	13: 62,171,255	H99Q	probably damaging	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
R0522:Spg20	UTSW	3	55128365	missense	probably damaging	1.00
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
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
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'- GTTTTGCTTTCAAGAAATGGCACAG -3'
(R):5'- AGGTGACTCCCAGGATTCTC -3'

Sequencing Primer
(F):5'- TGGCACAGACATCATATAACTTATCC -3'
(R):5'- GTGACTCCCAGGATTCTCATTATTTG -3'

Posted On

2017-02-10