Mutagenetix > Incidental Mutation

Incidental Mutation 'R0729:Spg7'

67395

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

038910-MU

Accession Numbers

Essential gene?

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

Stock #

R0729 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

123792247-123824499 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 123797156 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Aspartic acid at position 110 (N110D)

Ref Sequence

ENSEMBL: ENSMUSP00000104496 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000108868] [ENSMUST00000125975] [ENSMUST00000127664] [ENSMUST00000142541] [ENSMUST00000149248] [ENSMUST00000153285]

AlphaFold

Q3ULF4

Predicted Effect

probably damaging
Transcript: ENSMUST00000108868
AA Change: N110D

PolyPhen 2 Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000104496
Gene: ENSMUSG00000000738
AA Change: N110D

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 benign
Transcript: ENSMUST00000125975
AA Change: N5D

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000120361
Gene: ENSMUSG00000000738
AA Change: N5D

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

noncoding transcript
Transcript: ENSMUST00000128803

Predicted Effect

probably benign
Transcript: ENSMUST00000142541
AA Change: N5D

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

SMART Domains

Protein: ENSMUSP00000119017
Gene: ENSMUSG00000000738
AA Change: N5D

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: N110D

PolyPhen 2 Score 0.059 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000119552
Gene: ENSMUSG00000000738
AA Change: N110D

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: N110D

PolyPhen 2 Score 0.059 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000115039
Gene: ENSMUSG00000000738
AA Change: N110D

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

0.1129

Coding Region Coverage

1x: 99.4%
3x: 98.9%
10x: 97.8%
20x: 96.0%

Validation Efficiency

97% (74/76)

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: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933427D14Rik	C	A	11: 72,050,281 (GRCm39)	A828S	probably benign	Het
Acsm3	T	C	7: 119,383,207 (GRCm39)		probably benign	Het
Adamts12	G	A	15: 11,255,769 (GRCm39)	R446H	possibly damaging	Het
Adgrb1	A	G	15: 74,420,398 (GRCm39)	N849S	probably damaging	Het
Ankra2	A	G	13: 98,408,235 (GRCm39)	D228G	probably damaging	Het
Bicd1	T	C	6: 149,414,412 (GRCm39)	V375A	probably damaging	Het
Blvrb	A	G	7: 27,147,555 (GRCm39)	K5E	possibly damaging	Het
Cacna2d2	A	G	9: 107,394,456 (GRCm39)	N573D	probably benign	Het
Calhm2	C	A	19: 47,121,356 (GRCm39)	G271V	possibly damaging	Het
Capn13	C	T	17: 73,629,064 (GRCm39)	G581E	probably damaging	Het
Capzb	T	C	4: 139,016,288 (GRCm39)		probably benign	Het
Casd1	T	C	6: 4,619,753 (GRCm39)		probably benign	Het
Clca4b	A	G	3: 144,634,111 (GRCm39)		probably benign	Het
Col1a2	G	A	6: 4,518,822 (GRCm39)		probably benign	Het
Crx	A	G	7: 15,605,058 (GRCm39)		probably benign	Het
Cyp2c68	T	C	19: 39,727,994 (GRCm39)		probably benign	Het
Dcaf8	T	A	1: 172,000,221 (GRCm39)	D126E	probably benign	Het
Ddx31	T	C	2: 28,764,186 (GRCm39)	I464T	probably damaging	Het
Dhx32	G	A	7: 133,339,150 (GRCm39)	T155I	probably benign	Het
Elac2	C	A	11: 64,889,349 (GRCm39)	P567T	possibly damaging	Het
Fat4	A	G	3: 39,054,444 (GRCm39)		probably benign	Het
Fh1	T	G	1: 175,442,383 (GRCm39)	N156H	probably damaging	Het
Gm10064	T	C	5: 122,835,584 (GRCm39)		noncoding transcript	Het
Gm14137	A	G	2: 119,005,834 (GRCm39)	E131G	probably benign	Het
Gpr22	T	A	12: 31,759,312 (GRCm39)	K233M	probably damaging	Het
Gpr63	A	G	4: 25,007,480 (GRCm39)	N68S	probably benign	Het
Gypa	C	T	8: 81,223,421 (GRCm39)	P66S	unknown	Het
Htr2a	A	T	14: 74,879,587 (GRCm39)	Q72L	probably benign	Het
Klhdc7b	C	T	15: 89,271,598 (GRCm39)	R827*	probably null	Het
Leo1	G	A	9: 75,364,420 (GRCm39)	R520Q	possibly damaging	Het
Lrrc66	T	C	5: 73,765,757 (GRCm39)	M429V	probably benign	Het
Lrrc74a	C	T	12: 86,792,353 (GRCm39)	Q225*	probably null	Het
Mamdc4	T	A	2: 25,460,048 (GRCm39)	N68Y	probably damaging	Het
Map3k10	G	A	7: 27,360,992 (GRCm39)	P507L	probably damaging	Het
Methig1	T	A	15: 100,272,870 (GRCm39)	C68S	probably benign	Het
Metrn	C	T	17: 26,015,202 (GRCm39)		probably benign	Het
Mmp12	C	T	9: 7,358,290 (GRCm39)	T392I	possibly damaging	Het
Mss51	A	T	14: 20,533,160 (GRCm39)	I437N	probably damaging	Het
Mtus2	A	G	5: 148,014,097 (GRCm39)	T297A	probably benign	Het
Myo10	T	C	15: 25,722,243 (GRCm39)		probably benign	Het
Ncoa7	G	A	10: 30,567,575 (GRCm39)	P319S	probably benign	Het
Nlrp4d	A	T	7: 10,111,612 (GRCm39)		probably benign	Het
Obscn	A	G	11: 58,923,535 (GRCm39)	S6455P	probably damaging	Het
Or5b97	T	C	19: 12,878,259 (GRCm39)	N295S	probably damaging	Het
Or8b37	G	T	9: 37,959,123 (GRCm39)	V202L	probably benign	Het
Pcdh12	A	G	18: 38,415,517 (GRCm39)	I536T	probably benign	Het
Pex5l	G	T	3: 33,008,685 (GRCm39)		probably benign	Het
Pla2g2e	A	C	4: 138,608,046 (GRCm39)	K43Q	possibly damaging	Het
Rasa4	T	C	5: 136,130,924 (GRCm39)		probably benign	Het
Rsf1	C	T	7: 97,328,234 (GRCm39)	R1079W	probably damaging	Het
Sez6	A	G	11: 77,867,411 (GRCm39)	T803A	probably benign	Het
Shcbp1	T	A	8: 4,786,297 (GRCm39)	N602Y	probably benign	Het
Slc16a13	G	A	11: 70,109,857 (GRCm39)	P215S	probably damaging	Het
Slc39a6	T	C	18: 24,734,527 (GRCm39)	Q54R	probably benign	Het
Smg1	C	A	7: 117,745,512 (GRCm39)		probably benign	Het
Sptbn1	A	T	11: 30,060,902 (GRCm39)	S2010T	probably damaging	Het
Sun1	T	A	5: 139,223,619 (GRCm39)		probably benign	Het
Sytl5	A	G	X: 9,860,736 (GRCm39)	E717G	probably damaging	Het
Tle1	A	T	4: 72,044,679 (GRCm39)		probably benign	Het
Tm9sf4	T	A	2: 153,033,065 (GRCm39)	V290E	probably damaging	Het
Tmem63b	A	G	17: 45,985,060 (GRCm39)	S179P	probably damaging	Het
Trpm3	T	A	19: 22,965,153 (GRCm39)	F1549L	probably benign	Het
Ubr4	A	T	4: 139,212,631 (GRCm39)	Y5063F	possibly damaging	Het
Uroc1	T	A	6: 90,313,937 (GRCm39)	Y75N	probably damaging	Het
Vmn2r70	T	C	7: 85,215,112 (GRCm39)	T141A	probably benign	Het
Vps13c	A	G	9: 67,868,931 (GRCm39)	K3128E	probably damaging	Het
Wdr26	T	C	1: 181,013,470 (GRCm39)		probably null	Het
Wrn	T	A	8: 33,738,946 (GRCm39)		probably null	Het
Zfp106	C	T	2: 120,385,729 (GRCm39)	V13M	probably damaging	Het
Zfp456	G	A	13: 67,514,663 (GRCm39)	H348Y	probably damaging	Het
Zfpm1	G	A	8: 123,063,398 (GRCm39)	R819H	probably benign	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
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
R4952:Spg7	UTSW	8	123,816,910 (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'- GCTGTAATATCTCCGATGCAGCGAC -3'
(R):5'- ACTTTATTAAAACAGGGCCGCAGAAGTC -3'

Sequencing Primer
(F):5'- ATGCAGCGACTCTGAGAGC -3'
(R):5'- TAATCACAAAAGTAGGGCAGTTCAC -3'

Posted On

2013-09-03