Mutagenetix > Incidental Mutation

Incidental Mutation 'R4952:Spg7'

382065

Institutional Source

Beutler Lab

Gene Symbol

Spg7

Ensembl Gene

ENSMUSG00000000738

Gene Name

SPG7, paraplegin matrix AAA peptidase subunit

Synonyms

Cmar, paraplegin, spastic paraplegia 7 homolog (human)

MMRRC Submission

042549-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.121) question?

Stock #

R4952 (G1)

Quality Score

184

Status

Validated

Chromosome

Chromosomal Location

123792247-123824499 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 123816910 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Serine at position 534 (R534S)

Ref Sequence

ENSEMBL: ENSMUSP00000119552 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000108868] [ENSMUST00000125975] [ENSMUST00000127664] [ENSMUST00000135991] [ENSMUST00000149248] [ENSMUST00000153285]

AlphaFold

Q3ULF4

Predicted Effect

probably damaging
Transcript: ENSMUST00000108868
AA Change: R534S

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

SMART Domains

Protein: ENSMUSP00000104496
Gene: ENSMUSG00000000738
AA Change: R534S

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	5.2e-12	PFAM
transmembrane domain	250	272	N/A	INTRINSIC
AAA	341	481	1.96e-19	SMART
Pfam:Peptidase_M41	541	746	1.8e-74	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000125975
AA Change: R429S

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

SMART Domains

Protein: ENSMUSP00000120361
Gene: ENSMUSG00000000738
AA Change: R429S

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

unknown
Transcript: ENSMUST00000128234
AA Change: R102S

SMART Domains

Protein: ENSMUSP00000120793
Gene: ENSMUSG00000000738
AA Change: R102S

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: ENSMUST00000130787

Predicted Effect

probably benign
Transcript: ENSMUST00000135991

SMART Domains

Protein: ENSMUSP00000118066
Gene: ENSMUSG00000000738

Domain	Start	End	E-Value	Type
Pfam:Peptidase_M41	1	81	2.5e-30	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152972

Predicted Effect

probably damaging
Transcript: ENSMUST00000149248
AA Change: R534S

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

SMART Domains

Protein: ENSMUSP00000119552
Gene: ENSMUSG00000000738
AA Change: R534S

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

noncoding transcript
Transcript: ENSMUST00000142150

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000212364

Predicted Effect

probably benign
Transcript: ENSMUST00000153285

SMART Domains

Protein: ENSMUSP00000115039
Gene: ENSMUSG00000000738

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

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 99.0%
3x: 98.3%
10x: 96.5%
20x: 93.0%

Validation Efficiency

99% (93/94)

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: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930522L14Rik	A	G	5: 109,887,063 (GRCm39)		probably null	Het
4933421I07Rik	T	C	7: 42,097,083 (GRCm39)	Y76C	possibly damaging	Het
Adcy4	C	T	14: 56,016,486 (GRCm39)	D322N	probably damaging	Het
Ak9	A	G	10: 41,296,585 (GRCm39)	M1444V	probably benign	Het
Amfr	A	G	8: 94,699,787 (GRCm39)		probably benign	Het
Ankef1	A	G	2: 136,392,449 (GRCm39)	E546G	probably damaging	Het
Ankrd24	A	G	10: 81,482,982 (GRCm39)	M977V	probably benign	Het
Ap3m1	A	T	14: 21,090,134 (GRCm39)	S5T	probably benign	Het
Aqr	C	A	2: 113,940,418 (GRCm39)	D1243Y	probably damaging	Het
Arhgef2	T	C	3: 88,549,769 (GRCm39)	L591P	probably damaging	Het
Arid4a	C	A	12: 71,070,299 (GRCm39)	T70K	possibly damaging	Het
Asphd1	C	T	7: 126,547,857 (GRCm39)	A149T	probably benign	Het
Avpr1a	T	A	10: 122,285,659 (GRCm39)	M317K	probably damaging	Het
Birc2	T	C	9: 7,836,741 (GRCm39)	I109V	probably damaging	Het
Catsperd	A	G	17: 56,939,303 (GRCm39)	Y44C	probably damaging	Het
Crygb	T	G	1: 65,121,268 (GRCm39)	S20R	probably benign	Het
Cyp3a25	T	C	5: 145,928,334 (GRCm39)	N237S	probably benign	Het
Dkk3	C	T	7: 111,717,558 (GRCm39)	A304T	probably benign	Het
Dst	T	C	1: 34,310,503 (GRCm39)	L4101S	probably damaging	Het
Dysf	A	G	6: 84,126,968 (GRCm39)	N1407S	possibly damaging	Het
Epb41	A	G	4: 131,727,581 (GRCm39)	V265A	probably damaging	Het
Faim2	C	T	15: 99,419,109 (GRCm39)	E75K	possibly damaging	Het
Fam237b	T	A	5: 5,625,387 (GRCm39)	F28I	probably benign	Het
Fbn1	T	A	2: 125,159,454 (GRCm39)	D2208V	probably damaging	Het
Fbxo28	A	G	1: 182,153,950 (GRCm39)	S129P	probably damaging	Het
Fbxw14	T	A	9: 109,105,269 (GRCm39)	I299L	probably benign	Het
Fras1	C	T	5: 96,795,357 (GRCm39)	A1050V	probably benign	Het
Fyb1	C	A	15: 6,668,292 (GRCm39)	T495K	probably damaging	Het
Ghdc	A	T	11: 100,659,977 (GRCm39)	W257R	probably damaging	Het
Gm10719	T	C	9: 3,018,962 (GRCm39)	L69S	probably benign	Het
Gm12250	G	T	11: 58,079,210 (GRCm39)		noncoding transcript	Het
Gm4846	A	T	1: 166,311,503 (GRCm39)	F452Y	probably damaging	Het
Gpbp1	T	C	13: 111,577,284 (GRCm39)	D202G	probably damaging	Het
Gpd2	C	A	2: 57,197,025 (GRCm39)	Y193*	probably null	Het
Grhl2	G	T	15: 37,287,493 (GRCm39)	R229L	probably benign	Het
Gtf2a1	A	G	12: 91,542,523 (GRCm39)	F59L	possibly damaging	Het
Heatr1	G	T	13: 12,425,480 (GRCm39)	W640L	probably benign	Het
Kalrn	A	T	16: 34,177,785 (GRCm39)		probably null	Het
Keap1	T	C	9: 21,148,582 (GRCm39)	T142A	probably damaging	Het
Kpna2	G	A	11: 106,882,061 (GRCm39)	T255M	probably damaging	Het
Kpna3	A	G	14: 61,607,838 (GRCm39)	C456R	probably damaging	Het
Lama1	G	A	17: 68,074,561 (GRCm39)		probably null	Het
Lrrc37	T	C	11: 103,505,033 (GRCm39)	T2312A	possibly damaging	Het
Mag	C	A	7: 30,608,581 (GRCm39)	E178*	probably null	Het
Map3k13	A	G	16: 21,729,769 (GRCm39)	I467V	probably benign	Het
Mga	A	G	2: 119,733,782 (GRCm39)	E210G	probably damaging	Het
Msi2	C	T	11: 88,257,610 (GRCm39)		probably null	Het
Naa16	A	T	14: 79,582,525 (GRCm39)	D521E	probably damaging	Het
Nav2	C	T	7: 48,954,288 (GRCm39)		probably benign	Het
Nek10	T	A	14: 14,860,986 (GRCm38)	L513M	possibly damaging	Het
Nek5	T	C	8: 22,586,815 (GRCm39)	K332R	probably benign	Het
Nek5	T	A	8: 22,569,104 (GRCm39)	I573L	probably benign	Het
Ntn1	CCTTCTTCT	CCTTCT	11: 68,103,852 (GRCm39)		probably benign	Het
Odad1	A	C	7: 45,591,615 (GRCm39)	E293A	probably damaging	Het
Or2w1	G	A	13: 21,317,514 (GRCm39)	V190I	probably benign	Het
Or5v1b	A	T	17: 37,841,641 (GRCm39)	T258S	possibly damaging	Het
Or6c204	T	A	10: 129,022,466 (GRCm39)	T275S	probably benign	Het
Or8b12b	T	A	9: 37,684,360 (GRCm39)	M135K	probably damaging	Het
Orai1	T	G	5: 123,167,313 (GRCm39)	V162G	probably damaging	Het
P2rx6	T	C	16: 17,385,308 (GRCm39)	S134P	probably damaging	Het
Pappa2	G	A	1: 158,684,706 (GRCm39)	T811I	probably null	Het
Pcdhga10	T	C	18: 37,880,213 (GRCm39)		probably benign	Het
Pex16	C	T	2: 92,209,405 (GRCm39)	R241*	probably null	Het
Plxnb1	T	C	9: 108,943,904 (GRCm39)	F1969L	probably damaging	Het
Postn	A	G	3: 54,297,736 (GRCm39)		probably benign	Het
Prdm15	A	T	16: 97,607,277 (GRCm39)	I752N	probably damaging	Het
Rasgef1c	A	T	11: 49,870,339 (GRCm39)	K468M	probably damaging	Het
Rbfox1	A	G	16: 7,094,952 (GRCm39)	S111G	probably benign	Het
Rbm28	T	C	6: 29,138,597 (GRCm39)	D405G	probably damaging	Het
Rell1	A	G	5: 64,097,010 (GRCm39)		probably benign	Het
Rfx3	A	G	19: 27,808,072 (GRCm39)	S224P	probably damaging	Het
Scarb2	A	T	5: 92,602,636 (GRCm39)	I260K	probably damaging	Het
Septin4	A	G	11: 87,458,598 (GRCm39)	N324S	probably benign	Het
Slc15a4	A	G	5: 127,680,901 (GRCm39)	F72L	probably damaging	Het
Stoml2	T	C	4: 43,029,589 (GRCm39)	T164A	probably benign	Het
Syt11	C	T	3: 88,669,590 (GRCm39)	G101S	possibly damaging	Het
Traj12	A	G	14: 54,444,013 (GRCm39)		probably benign	Het
Traj7	A	T	14: 54,448,981 (GRCm39)		probably benign	Het
Tysnd1	C	T	10: 61,537,855 (GRCm39)	T175I	possibly damaging	Het
Usp48	T	G	4: 137,334,004 (GRCm39)	Y139*	probably null	Het
Vmn2r72	A	G	7: 85,400,317 (GRCm39)	L244P	probably benign	Het
Wasf1	C	A	10: 40,812,186 (GRCm39)	P325Q	unknown	Het
Zc3h18	T	A	8: 123,137,639 (GRCm39)		probably benign	Het
Zfp712	A	G	13: 67,188,905 (GRCm39)	S541P	possibly damaging	Het

Other mutations in Spg7

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01862:Spg7	APN	8	123,803,669 (GRCm39)	missense	probably damaging	1.00
IGL01868:Spg7	APN	8	123,816,975 (GRCm39)	critical splice donor site	probably null
IGL02551:Spg7	APN	8	123,803,717 (GRCm39)	missense	probably damaging	1.00
IGL02744:Spg7	APN	8	123,820,400 (GRCm39)	missense	probably damaging	1.00
IGL03161:Spg7	APN	8	123,814,070 (GRCm39)	missense	probably damaging	1.00
IGL03165:Spg7	APN	8	123,807,551 (GRCm39)	critical splice donor site	probably null
R0729:Spg7	UTSW	8	123,797,156 (GRCm39)	missense	probably damaging	0.96
R1580:Spg7	UTSW	8	123,816,977 (GRCm39)	unclassified	probably benign
R1696:Spg7	UTSW	8	123,816,964 (GRCm39)	missense	probably benign	0.05
R1909:Spg7	UTSW	8	123,807,480 (GRCm39)	missense	probably benign	0.01
R3751:Spg7	UTSW	8	123,814,112 (GRCm39)	missense	probably damaging	1.00
R3753:Spg7	UTSW	8	123,814,112 (GRCm39)	missense	probably damaging	1.00
R3921:Spg7	UTSW	8	123,814,112 (GRCm39)	missense	probably damaging	1.00
R3976:Spg7	UTSW	8	123,806,187 (GRCm39)	missense	probably damaging	1.00
R4908:Spg7	UTSW	8	123,807,394 (GRCm39)	missense	probably damaging	1.00
R5392:Spg7	UTSW	8	123,814,102 (GRCm39)	missense	probably damaging	1.00
R5637:Spg7	UTSW	8	123,821,314 (GRCm39)	missense	possibly damaging	0.82
R5684:Spg7	UTSW	8	123,800,623 (GRCm39)	missense	probably damaging	0.99
R5810:Spg7	UTSW	8	123,821,308 (GRCm39)	missense	possibly damaging	0.94
R6452:Spg7	UTSW	8	123,806,162 (GRCm39)	missense	possibly damaging	0.54
R6453:Spg7	UTSW	8	123,806,162 (GRCm39)	missense	possibly damaging	0.54
R6454:Spg7	UTSW	8	123,806,162 (GRCm39)	missense	possibly damaging	0.54
R6750:Spg7	UTSW	8	123,800,650 (GRCm39)	missense	probably damaging	1.00
R7090:Spg7	UTSW	8	123,818,491 (GRCm39)	critical splice donor site	probably null
R7213:Spg7	UTSW	8	123,816,971 (GRCm39)	missense	probably damaging	1.00
R7705:Spg7	UTSW	8	123,800,617 (GRCm39)	missense	possibly damaging	0.63
R7811:Spg7	UTSW	8	123,824,164 (GRCm39)	missense	possibly damaging	0.89
R7863:Spg7	UTSW	8	123,815,788 (GRCm39)	critical splice donor site	probably null
R8375:Spg7	UTSW	8	123,800,568 (GRCm39)	missense	probably damaging	0.99
R9228:Spg7	UTSW	8	123,807,408 (GRCm39)	missense	possibly damaging	0.94
R9321:Spg7	UTSW	8	123,803,688 (GRCm39)	missense	probably benign	0.22
R9508:Spg7	UTSW	8	123,800,623 (GRCm39)	missense	probably damaging	0.99
Z1177:Spg7	UTSW	8	123,816,962 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CATGTGCTGTCAGGTGATGC -3'
(R):5'- GTAACAATTCCCTCGCTACGTAC -3'

Sequencing Primer
(F):5'- TGCTATTTGGAGACAGAGCCC -3'
(R):5'- CGCTACGTACCTCATTAGAATATTTC -3'

Posted On

2016-04-27