Mutagenetix > Incidental Mutation

Incidental Mutation 'R1909:Spg7'

210171

Institutional Source

Beutler Lab

Gene Symbol

Spg7

Ensembl Gene

ENSMUSG00000000738

Gene Name

SPG7, paraplegin matrix AAA peptidase subunit

Synonyms

Cmar, paraplegin

MMRRC Submission

039928-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.124) question?

Stock #

R1909 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

123062942-123097760 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 123080741 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 419 (T419A)

Ref Sequence

ENSEMBL: ENSMUSP00000119552 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000125975] [ENSMUST00000127664] [ENSMUST00000142541] [ENSMUST00000149248] [ENSMUST00000153285]

AlphaFold

Q3ULF4

Predicted Effect

probably benign
Transcript: ENSMUST00000125975
AA Change: T314A

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000120361
Gene: ENSMUSG00000000738
AA Change: T314A

Domain	Start	End	E-Value	Type
low complexity region	17	30	N/A	INTRINSIC
Pfam:FtsH_ext	37	137	8.5e-12	PFAM
transmembrane domain	145	167	N/A	INTRINSIC
AAA	236	376	1.96e-19	SMART
Pfam:Peptidase_M41	436	641	9.8e-74	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000127664

SMART Domains

Protein: ENSMUSP00000118564
Gene: ENSMUSG00000092329

Domain	Start	End	E-Value	Type
Pfam:Glycos_transf_2	104	287	7.4e-31	PFAM
Pfam:Glyco_transf_7C	261	331	4.9e-8	PFAM
RICIN	406	531	9.28e-27	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000128234

SMART Domains

Protein: ENSMUSP00000120793
Gene: ENSMUSG00000000738

Domain	Start	End	E-Value	Type
Pfam:AAA	1	48	5.8e-10	PFAM
Pfam:Peptidase_M41	110	222	9.7e-43	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128803

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142150

Predicted Effect

probably benign
Transcript: ENSMUST00000142541

SMART Domains

Protein: ENSMUSP00000119017
Gene: ENSMUSG00000000738

Domain	Start	End	E-Value	Type
low complexity region	17	30	N/A	INTRINSIC
Pfam:FtsH_ext	37	137	1.2e-12	PFAM
transmembrane domain	145	167	N/A	INTRINSIC
PDB:2QZ4\|A	200	230	2e-12	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000149248
AA Change: T419A

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000119552
Gene: ENSMUSG00000000738
AA Change: T419A

Domain	Start	End	E-Value	Type
low complexity region	5	60	N/A	INTRINSIC
low complexity region	122	135	N/A	INTRINSIC
Pfam:FtsH_ext	142	242	3.9e-11	PFAM
transmembrane domain	250	272	N/A	INTRINSIC
AAA	341	481	1.96e-19	SMART
Pfam:Peptidase_M41	541	746	7e-75	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000153285
AA Change: T419A

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000115039
Gene: ENSMUSG00000000738
AA Change: T419A

Domain	Start	End	E-Value	Type
low complexity region	5	60	N/A	INTRINSIC
low complexity region	122	135	N/A	INTRINSIC
Pfam:FtsH_ext	142	242	3.8e-11	PFAM
transmembrane domain	250	272	N/A	INTRINSIC
AAA	341	481	1.96e-19	SMART
Pfam:Peptidase_M41	515	709	2.5e-68	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000153492

SMART Domains

Protein: ENSMUSP00000133602
Gene: ENSMUSG00000000738

Domain	Start	End	E-Value	Type
Pfam:FtsH_ext	1	102	1.3e-12	PFAM
transmembrane domain	110	132	N/A	INTRINSIC
PDB:2QZ4\|A	165	192	1e-8	PDB

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 95.4%
20x: 93.1%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a mitochondrial metalloprotease protein that is a member of the AAA family. Members of this protein family share an ATPase domain and have roles in diverse cellular processes including membrane trafficking, intracellular motility, organelle biogenesis, protein folding, and proteolysis. Mutations in this gene cause autosomal recessive spastic paraplegia 7. Two transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Mar 2014]
PHENOTYPE: Homozygous null mice exhibit impaired motor skills, putativley associated with axonal degeneration in the central and peripheral nervous systems. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 112 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4931406P16Rik	T	A	7: 34,258,036	I59L	probably benign	Het
9530053A07Rik	T	C	7: 28,144,348	V887A	possibly damaging	Het
Aarsd1	A	C	11: 101,410,231		probably null	Het
Abcc5	A	G	16: 20,376,509		probably null	Het
Abcc6	T	C	7: 46,020,134		probably null	Het
Adam15	C	A	3: 89,345,330	M317I	probably benign	Het
Ago3	T	C	4: 126,346,737	T111A	probably damaging	Het
Amz1	G	T	5: 140,752,461	S492I	probably benign	Het
Arid1a	T	C	4: 133,693,761	N911S	unknown	Het
Arntl2	A	T	6: 146,810,810	E111V	probably benign	Het
Ascl2	C	A	7: 142,968,163	A115S	probably damaging	Het
Ash1l	T	C	3: 88,984,528	V1238A	probably benign	Het
Asxl2	G	T	12: 3,474,577	V202F	probably damaging	Het
Atp10a	A	T	7: 58,828,712	Q1501L	probably benign	Het
Avpr1a	A	T	10: 122,452,208	I374L	probably benign	Het
Bmx	T	C	X: 164,239,415	H157R	probably benign	Het
Camk4	T	A	18: 33,158,816		probably null	Het
Ccdc103	G	A	11: 102,882,566	D5N	probably benign	Het
Ccdc186	A	T	19: 56,793,361	N70K	probably damaging	Het
Cebpz	A	T	17: 78,934,907	Y439*	probably null	Het
Cfap206	A	C	4: 34,722,714	S122R	probably benign	Het
Cnst	T	C	1: 179,622,791	S607P	probably damaging	Het
Col8a2	C	A	4: 126,312,133	D645E	possibly damaging	Het
Cpsf4l	A	T	11: 113,703,378		probably null	Het
Crim1	C	T	17: 78,313,127	T332I	probably benign	Het
Csmd1	A	T	8: 15,906,116	Y3364N	probably damaging	Het
D5Ertd579e	A	T	5: 36,614,058	S998T	probably benign	Het
Dab2ip	C	G	2: 35,718,815	A587G	probably damaging	Het
Dach1	C	T	14: 97,901,393	G486D	probably damaging	Het
Ddx24	T	C	12: 103,409,982	I752V	probably damaging	Het
Dhx33	A	G	11: 70,989,107	V359A	probably benign	Het
Dip2c	A	T	13: 9,533,350	T123S	probably benign	Het
Dync1h1	G	A	12: 110,662,629	E4207K	probably damaging	Het
Eef1b2	G	T	1: 63,177,272	D21Y	probably damaging	Het
Eif3b	T	C	5: 140,432,937	S462P	probably damaging	Het
Elmod2	G	C	8: 83,316,369	R277G	probably benign	Het
Epg5	T	A	18: 77,959,032	D555E	probably benign	Het
Ercc8	A	T	13: 108,175,566	K172*	probably null	Het
Fat3	T	C	9: 15,998,115	N2197S	probably benign	Het
Fbf1	A	G	11: 116,145,992	V972A	possibly damaging	Het
Fes	T	C	7: 80,386,861	R113G	probably damaging	Het
Fzd1	G	T	5: 4,757,481	H34N	probably benign	Het
Galnt17	T	A	5: 131,111,838	Y147F	probably benign	Het
Gdf6	T	C	4: 9,859,971	L351P	probably damaging	Het
Gm10277	TC	T	11: 77,786,002		probably null	Het
Gm15448	A	T	7: 3,822,919	I317N	probably benign	Het
Gm2381	A	T	7: 42,819,928	H257Q	probably damaging	Het
Gm6904	A	T	14: 59,258,613	S17R	probably benign	Het
Gm9844	T	C	7: 24,862,306	I10T	possibly damaging	Het
Hivep1	A	T	13: 42,155,646	K454M	probably benign	Het
Hmmr	T	A	11: 40,708,098	E566D	probably damaging	Het
Hydin	T	G	8: 110,587,772	V4296G	probably damaging	Het
Il18r1	T	A	1: 40,474,914	D93E	probably damaging	Het
Iqgap1	T	C	7: 80,743,828	D667G	probably benign	Het
Lama3	T	C	18: 12,581,798	I3278T	probably benign	Het
Lrp4	T	A	2: 91,498,408	V1551D	possibly damaging	Het
Mdn1	CGGAGGAGGAGGAGGAG	CGGAGGAGGAGGAG	4: 32,760,839		probably benign	Het
Mga	T	A	2: 119,926,594	H1018Q	possibly damaging	Het
Ncoa7	A	T	10: 30,689,800	M666K	probably damaging	Het
Ndnf	T	G	6: 65,703,313	V192G	possibly damaging	Het
Nr4a1	T	A	15: 101,274,227	I594N	probably damaging	Het
Olfr1294	T	A	2: 111,538,014	I92F	probably damaging	Het
Olfr60	T	C	7: 140,345,465	I175V	probably benign	Het
Olfr618	A	G	7: 103,597,343	N9S	probably benign	Het
Olfr635	G	A	7: 103,979,790	W199*	probably null	Het
Olfr698	T	C	7: 106,752,995	N131S	probably benign	Het
Paxbp1	T	C	16: 91,044,305		probably benign	Het
Pcdhb8	A	G	18: 37,355,962	E231G	possibly damaging	Het
Pcsk5	A	T	19: 17,433,461	Y1856N	probably benign	Het
Pde3a	T	C	6: 141,250,239	V217A	probably benign	Het
Pirb	A	T	7: 3,714,588	D674E	probably benign	Het
Pnisr	T	A	4: 21,869,517	M335K	possibly damaging	Het
Pnpla7	T	A	2: 24,997,288	M48K	possibly damaging	Het
Pomgnt2	A	T	9: 121,982,191	I508N	possibly damaging	Het
Ppp2r5e	C	G	12: 75,469,567	A239P	probably damaging	Het
Prkca	A	T	11: 107,939,612	D217E	possibly damaging	Het
Rac3	A	C	11: 120,723,337	I142L	probably benign	Het
Ralgapb	G	T	2: 158,444,675	A347S	probably damaging	Het
Rbm43	G	C	2: 51,925,434	S258R	possibly damaging	Het
Rnf182	T	A	13: 43,668,423	V150E	probably benign	Het
Rsph10b	T	C	5: 143,985,491	F409L	probably benign	Het
Ryr2	A	T	13: 11,700,349	L2778M	probably damaging	Het
Scn1a	T	C	2: 66,331,352	N284S	possibly damaging	Het
Scyl2	A	T	10: 89,640,905	M786K	probably benign	Het
Sema4g	C	A	19: 44,997,622	R301S	probably damaging	Het
Senp6	A	T	9: 80,113,774	E245D	possibly damaging	Het
Setx	T	C	2: 29,163,009	V2095A	possibly damaging	Het
Slc13a2	A	T	11: 78,400,142	M412K	possibly damaging	Het
Slc25a4	T	C	8: 46,209,400	N74D	probably damaging	Het
Slc28a1	T	A	7: 81,142,035	F316L	probably damaging	Het
Slfn8	G	A	11: 83,003,621	Q731*	probably null	Het
Slitrk4	A	G	X: 64,272,623	I146T	probably damaging	Het
Smg1	A	G	7: 118,154,199		probably benign	Het
Smg8	G	T	11: 87,080,613	Y777*	probably null	Het
Smyd1	T	A	6: 71,239,579	K61N	probably benign	Het
Sod2	T	C	17: 13,015,169	*223R	probably null	Het
Sp6	G	T	11: 97,021,508	A16S	probably benign	Het
Spata31d1a	A	C	13: 59,702,695	Y540D	probably damaging	Het
Spatc1l	A	G	10: 76,563,917	D91G	probably damaging	Het
St5	G	A	7: 109,525,326	Q686*	probably null	Het
St8sia4	A	G	1: 95,627,573	I244T	probably damaging	Het
Tbl2	C	T	5: 135,152,991	R27W	probably damaging	Het
Tmed4	G	A	11: 6,274,694	P47L	probably damaging	Het
Tmtc1	T	C	6: 148,444,048	D51G	possibly damaging	Het
Ttc28	T	C	5: 111,284,054		probably null	Het
Unc13d	A	G	11: 116,070,295	F412S	probably damaging	Het
Unc45b	A	C	11: 82,926,087	K451T	probably damaging	Het
Vmn2r16	A	G	5: 109,363,987	M687V	probably benign	Het
Vmn2r68	T	A	7: 85,234,052	H164L	probably benign	Het
Vps51	A	G	19: 6,069,469	V625A	probably benign	Het
Wapl	T	A	14: 34,691,912	W244R	probably damaging	Het
Wdr75	C	T	1: 45,823,403	T794I	probably benign	Het

Other mutations in Spg7

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01862:Spg7	APN	8	123076930	missense	probably damaging	1.00
IGL01868:Spg7	APN	8	123090236	critical splice donor site	probably null
IGL02551:Spg7	APN	8	123076978	missense	probably damaging	1.00
IGL02744:Spg7	APN	8	123093661	missense	probably damaging	1.00
IGL03161:Spg7	APN	8	123087331	missense	probably damaging	1.00
IGL03165:Spg7	APN	8	123080812	critical splice donor site	probably null
R0729:Spg7	UTSW	8	123070417	missense	probably damaging	0.96
R1580:Spg7	UTSW	8	123090238	unclassified	probably benign
R1696:Spg7	UTSW	8	123090225	missense	probably benign	0.05
R3751:Spg7	UTSW	8	123087373	missense	probably damaging	1.00
R3753:Spg7	UTSW	8	123087373	missense	probably damaging	1.00
R3921:Spg7	UTSW	8	123087373	missense	probably damaging	1.00
R3976:Spg7	UTSW	8	123079448	missense	probably damaging	1.00
R4908:Spg7	UTSW	8	123080655	missense	probably damaging	1.00
R4952:Spg7	UTSW	8	123090171	missense	probably damaging	1.00
R5392:Spg7	UTSW	8	123087363	missense	probably damaging	1.00
R5637:Spg7	UTSW	8	123094575	missense	possibly damaging	0.82
R5684:Spg7	UTSW	8	123073884	missense	probably damaging	0.99
R5810:Spg7	UTSW	8	123094569	missense	possibly damaging	0.94
R6452:Spg7	UTSW	8	123079423	missense	possibly damaging	0.54
R6453:Spg7	UTSW	8	123079423	missense	possibly damaging	0.54
R6454:Spg7	UTSW	8	123079423	missense	possibly damaging	0.54
R6750:Spg7	UTSW	8	123073911	missense	probably damaging	1.00
R7090:Spg7	UTSW	8	123091752	critical splice donor site	probably null
R7213:Spg7	UTSW	8	123090232	missense	probably damaging	1.00
R7705:Spg7	UTSW	8	123073878	missense	possibly damaging	0.63
R7811:Spg7	UTSW	8	123097425	missense	possibly damaging	0.89
R7863:Spg7	UTSW	8	123089049	critical splice donor site	probably null
R8375:Spg7	UTSW	8	123073829	missense	probably damaging	0.99
R9228:Spg7	UTSW	8	123080669	missense	possibly damaging	0.94
R9321:Spg7	UTSW	8	123076949	missense	probably benign	0.22
R9508:Spg7	UTSW	8	123073884	missense	probably damaging	0.99
Z1177:Spg7	UTSW	8	123090223	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TAGCAAGATGCCAGCTACTTC -3'
(R):5'- TGCCCTAGGAGCTAGAAGAG -3'

Sequencing Primer
(F):5'- GAAGATTTTGCCAGGCTGTAACCC -3'
(R):5'- GAGAAACCGTGACCTGATCCG -3'

Posted On

2014-06-30