Mutagenetix > Incidental Mutation

Incidental Mutation 'R5354:Synpo'

424013

Institutional Source

Beutler Lab

Gene Symbol

Synpo

Ensembl Gene

ENSMUSG00000043079

Gene Name

synaptopodin

Synonyms

9030217H17Rik, 9330140I15Rik

MMRRC Submission

042933-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.238) question?

Stock #

R5354 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

60727045-60793214 bp(-) (GRCm39)

Type of Mutation

critical splice donor site (2 bp from exon)

DNA Base Change (assembly)

A to G at 60735303 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000115355 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000097566] [ENSMUST00000115318] [ENSMUST00000123288] [ENSMUST00000130044] [ENSMUST00000130360] [ENSMUST00000143275] [ENSMUST00000155195]

AlphaFold

Q8CC35

Predicted Effect

probably benign
Transcript: ENSMUST00000097566
AA Change: V642A

PolyPhen 2 Score 0.105 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000095174
Gene: ENSMUSG00000043079
AA Change: V642A

Domain	Start	End	E-Value	Type
low complexity region	78	90	N/A	INTRINSIC
low complexity region	328	341	N/A	INTRINSIC
low complexity region	428	446	N/A	INTRINSIC
low complexity region	571	600	N/A	INTRINSIC
low complexity region	607	628	N/A	INTRINSIC
low complexity region	714	741	N/A	INTRINSIC
low complexity region	769	782	N/A	INTRINSIC
low complexity region	786	811	N/A	INTRINSIC
low complexity region	830	846	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000115318
AA Change: V642A

PolyPhen 2 Score 0.653 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000110973
Gene: ENSMUSG00000043079
AA Change: V642A

Domain	Start	End	E-Value	Type
low complexity region	78	90	N/A	INTRINSIC
low complexity region	328	341	N/A	INTRINSIC
low complexity region	428	446	N/A	INTRINSIC
low complexity region	571	600	N/A	INTRINSIC
low complexity region	607	628	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000123288

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128528

Predicted Effect

probably benign
Transcript: ENSMUST00000130044
AA Change: V642A

PolyPhen 2 Score 0.105 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000121756
Gene: ENSMUSG00000043079
AA Change: V642A

Domain	Start	End	E-Value	Type
low complexity region	78	90	N/A	INTRINSIC
low complexity region	328	341	N/A	INTRINSIC
low complexity region	428	446	N/A	INTRINSIC
low complexity region	571	600	N/A	INTRINSIC
low complexity region	607	628	N/A	INTRINSIC
low complexity region	714	741	N/A	INTRINSIC
low complexity region	769	782	N/A	INTRINSIC
low complexity region	786	811	N/A	INTRINSIC
low complexity region	830	846	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000130360

SMART Domains

Protein: ENSMUSP00000115355
Gene: ENSMUSG00000043079

Domain	Start	End	E-Value	Type
low complexity region	33	43	N/A	INTRINSIC
low complexity region	208	232	N/A	INTRINSIC
low complexity region	317	329	N/A	INTRINSIC
low complexity region	567	580	N/A	INTRINSIC
low complexity region	667	685	N/A	INTRINSIC
low complexity region	810	839	N/A	INTRINSIC
low complexity region	846	867	N/A	INTRINSIC
low complexity region	913	940	N/A	INTRINSIC
low complexity region	968	981	N/A	INTRINSIC
low complexity region	985	1010	N/A	INTRINSIC
low complexity region	1029	1045	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137894

Predicted Effect

possibly damaging
Transcript: ENSMUST00000143275
AA Change: V881A

PolyPhen 2 Score 0.653 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000125272
Gene: ENSMUSG00000043079
AA Change: V881A

Domain	Start	End	E-Value	Type
low complexity region	33	43	N/A	INTRINSIC
low complexity region	208	232	N/A	INTRINSIC
low complexity region	317	329	N/A	INTRINSIC
low complexity region	567	580	N/A	INTRINSIC
low complexity region	667	685	N/A	INTRINSIC
low complexity region	810	839	N/A	INTRINSIC
low complexity region	846	867	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000155195
AA Change: V642A

PolyPhen 2 Score 0.653 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000117897
Gene: ENSMUSG00000043079
AA Change: V642A

Domain	Start	End	E-Value	Type
low complexity region	78	90	N/A	INTRINSIC
low complexity region	328	341	N/A	INTRINSIC
low complexity region	428	446	N/A	INTRINSIC
low complexity region	571	600	N/A	INTRINSIC
low complexity region	607	628	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160395

Meta Mutation Damage Score

0.0994

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.3%
20x: 95.4%

Validation Efficiency

100% (80/80)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Synaptopodin is an actin-associated protein that may play a role in actin-based cell shape and motility. The name synaptopodin derives from the protein's associations with postsynaptic densities and dendritic spines and with renal podocytes (Mundel et al., 1997 [PubMed 9314539]).[supplied by OMIM, Mar 2008]
PHENOTYPE: Mice homozygous for disruptions in this gene display abnormalities in telencephalic neurons, reduced long term potentiation, and behavioral abnormalities including hypoactivity, reduced anxiety, and learning deficiencies. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A630010A05Rik	A	G	16: 14,436,535 (GRCm39)	K196R	probably benign	Het
Ablim1	T	C	19: 57,119,355 (GRCm39)	E243G	probably benign	Het
Acat1	T	A	9: 53,500,483 (GRCm39)	E271V	possibly damaging	Het
Aco1	T	C	4: 40,180,290 (GRCm39)		probably null	Het
Adam22	C	A	5: 8,140,182 (GRCm39)	G202W	probably damaging	Het
Agbl3	T	A	6: 34,791,687 (GRCm39)	H596Q	probably benign	Het
Anxa7	A	G	14: 20,514,977 (GRCm39)	L177P	possibly damaging	Het
Atp11a	A	T	8: 12,856,753 (GRCm39)	N48I	probably damaging	Het
Bcas1	T	A	2: 170,191,316 (GRCm39)	N492I	possibly damaging	Het
Bclaf1	A	G	10: 20,209,278 (GRCm39)	Y498C	probably damaging	Het
Bltp3a	G	A	17: 28,106,489 (GRCm39)	S1005N	probably benign	Het
Bod1l	A	C	5: 41,988,880 (GRCm39)	V409G	probably damaging	Het
Ccdc170	G	A	10: 4,484,188 (GRCm39)	C338Y	probably benign	Het
Cdc45	C	T	16: 18,614,647 (GRCm39)	R205H	probably damaging	Het
Ckap2	A	C	8: 22,667,581 (GRCm39)	N93K	probably damaging	Het
Clca3a1	A	T	3: 144,442,766 (GRCm39)	S759R	possibly damaging	Het
Coro1c	A	T	5: 113,984,226 (GRCm39)	I347N	possibly damaging	Het
Cpox	A	G	16: 58,491,205 (GRCm39)	T139A	probably damaging	Het
Cyp4a12b	C	A	4: 115,290,661 (GRCm39)		probably null	Het
Dctn1	T	G	6: 83,160,108 (GRCm39)	V116G	possibly damaging	Het
Dhx38	A	G	8: 110,282,378 (GRCm39)	V683A	probably damaging	Het
Dnah12	G	A	14: 26,496,299 (GRCm39)		probably null	Het
Dnajb7	T	C	15: 81,292,208 (GRCm39)	E43G	probably damaging	Het
Dsc1	A	T	18: 20,220,632 (GRCm39)	V714E	probably damaging	Het
Dusp29	G	A	14: 21,727,091 (GRCm39)	R186W	probably benign	Het
Egfem1	T	C	3: 29,136,361 (GRCm39)		probably null	Het
Fchsd1	C	T	18: 38,092,926 (GRCm39)		probably benign	Het
Fmo1	T	C	1: 162,657,714 (GRCm39)	T476A	probably benign	Het
Gm10237	T	C	16: 35,741,099 (GRCm39)		noncoding transcript	Het
Gm14496	A	G	2: 181,642,602 (GRCm39)	S758G	probably damaging	Het
Gpat2	T	A	2: 127,270,643 (GRCm39)	L97Q	probably damaging	Het
Gpr162	T	C	6: 124,836,600 (GRCm39)	D357G	probably benign	Het
Hax1	A	T	3: 89,905,262 (GRCm39)	D34E	probably damaging	Het
Hmgcr	C	T	13: 96,791,404 (GRCm39)	V97M	probably benign	Het
Hsd3b2	T	C	3: 98,619,631 (GRCm39)	T105A	probably benign	Het
Ints1	A	G	5: 139,752,183 (GRCm39)		probably null	Het
Islr	T	C	9: 58,064,895 (GRCm39)	E204G	probably damaging	Het
Lrrc36	A	G	8: 106,151,996 (GRCm39)	N60D	probably damaging	Het
Maf1	T	C	15: 76,237,330 (GRCm39)		probably benign	Het
Mrgprb4	T	A	7: 47,848,077 (GRCm39)	R284W	probably benign	Het
Myh4	A	T	11: 67,146,551 (GRCm39)	N1508I	possibly damaging	Het
Nufip2	A	G	11: 77,577,103 (GRCm39)	H17R	unknown	Het
Oasl1	A	T	5: 115,075,055 (GRCm39)	I372L	probably damaging	Het
Or5ae1	T	A	7: 84,565,357 (GRCm39)	Y123*	probably null	Het
Or6p1	T	C	1: 174,258,252 (GRCm39)	L86P	probably damaging	Het
Pald1	A	T	10: 61,184,440 (GRCm39)	Y226N	probably damaging	Het
Pcdhb13	G	T	18: 37,577,844 (GRCm39)	G741C	probably damaging	Het
Pcdhga10	A	G	18: 37,881,259 (GRCm39)	D340G	probably damaging	Het
Pclo	C	A	5: 14,728,822 (GRCm39)		probably benign	Het
Pcsk4	G	T	10: 80,159,523 (GRCm39)	N416K	probably damaging	Het
Pde10a	C	A	17: 9,180,812 (GRCm39)	R398S	probably damaging	Het
Plin1	T	A	7: 79,375,469 (GRCm39)	T227S	possibly damaging	Het
Pnpt1	A	G	11: 29,104,166 (GRCm39)	D542G	probably damaging	Het
Ppp4r3b	T	A	11: 29,161,646 (GRCm39)	D673E	probably benign	Het
Prr18	C	A	17: 8,559,892 (GRCm39)	P16Q	probably damaging	Het
Psmc3	T	A	2: 90,889,698 (GRCm39)	Y440N	probably damaging	Het
Rassf5	T	C	1: 131,108,385 (GRCm39)	I232V	probably benign	Het
Rims1	T	A	1: 22,577,592 (GRCm39)	D218V	probably damaging	Het
Skint10	T	C	4: 112,568,790 (GRCm39)	N309S	possibly damaging	Het
Slc6a1	T	C	6: 114,279,584 (GRCm39)	M121T	possibly damaging	Het
Slit3	A	G	11: 35,566,740 (GRCm39)	D1004G	probably damaging	Het
Snap91	C	T	9: 86,717,177 (GRCm39)	V215I	possibly damaging	Het
Son	T	C	16: 91,452,627 (GRCm39)	L458S	probably damaging	Het
St18	C	T	1: 6,914,395 (GRCm39)	A782V	probably damaging	Het
Thbs3	A	G	3: 89,128,684 (GRCm39)	D458G	probably damaging	Het
Tpr	C	T	1: 150,321,675 (GRCm39)	R3C	probably damaging	Het
Trp63	A	G	16: 25,503,105 (GRCm39)		probably null	Het
Vmn1r27	C	A	6: 58,192,581 (GRCm39)	R141L	probably benign	Het
Wnk1	T	C	6: 119,945,484 (GRCm39)	I699V	probably benign	Het
Xkr6	A	G	14: 64,056,353 (GRCm39)	D88G	possibly damaging	Het
Zan	A	G	5: 137,379,050 (GRCm39)		probably benign	Het
Zbtb7b	T	C	3: 89,286,913 (GRCm39)		probably benign	Het
Zfp618	A	T	4: 62,998,265 (GRCm39)	D33V	probably damaging	Het

Other mutations in Synpo

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00725:Synpo	APN	18	60,737,149 (GRCm39)	missense	probably damaging	1.00
IGL00976:Synpo	APN	18	60,736,491 (GRCm39)	missense	possibly damaging	0.74
IGL01808:Synpo	APN	18	60,735,280 (GRCm39)	missense	probably benign	0.01
IGL02116:Synpo	APN	18	60,736,528 (GRCm39)	missense	probably damaging	1.00
IGL02444:Synpo	APN	18	60,735,502 (GRCm39)	missense	probably damaging	1.00
IGL02838:Synpo	APN	18	60,736,872 (GRCm39)	missense	probably damaging	1.00
R0420:Synpo	UTSW	18	60,735,490 (GRCm39)	missense	probably damaging	0.97
R0650:Synpo	UTSW	18	60,735,412 (GRCm39)	missense	possibly damaging	0.83
R0790:Synpo	UTSW	18	60,736,575 (GRCm39)	missense	probably damaging	0.98
R1213:Synpo	UTSW	18	60,735,525 (GRCm39)	missense	possibly damaging	0.83
R1695:Synpo	UTSW	18	60,736,459 (GRCm39)	missense	probably benign	0.00
R1763:Synpo	UTSW	18	60,735,856 (GRCm39)	missense	probably damaging	1.00
R1920:Synpo	UTSW	18	60,736,661 (GRCm39)	missense	probably benign	0.00
R1921:Synpo	UTSW	18	60,736,661 (GRCm39)	missense	probably benign	0.00
R2133:Synpo	UTSW	18	60,735,967 (GRCm39)	missense	probably damaging	1.00
R3757:Synpo	UTSW	18	60,736,062 (GRCm39)	missense	probably damaging	1.00
R4796:Synpo	UTSW	18	60,737,386 (GRCm39)	missense	probably damaging	0.97
R4841:Synpo	UTSW	18	60,736,684 (GRCm39)	missense	probably damaging	0.99
R4842:Synpo	UTSW	18	60,736,684 (GRCm39)	missense	probably damaging	0.99
R4911:Synpo	UTSW	18	60,762,936 (GRCm39)	utr 5 prime	probably benign
R5091:Synpo	UTSW	18	60,735,831 (GRCm39)	nonsense	probably null
R5327:Synpo	UTSW	18	60,736,918 (GRCm39)	missense	possibly damaging	0.93
R5671:Synpo	UTSW	18	60,729,022 (GRCm39)	missense	probably damaging	0.99
R5868:Synpo	UTSW	18	60,737,118 (GRCm39)	missense	probably damaging	1.00
R6007:Synpo	UTSW	18	60,736,687 (GRCm39)	missense	probably benign	0.35
R7266:Synpo	UTSW	18	60,762,631 (GRCm39)	missense	probably benign	0.00
R7472:Synpo	UTSW	18	60,762,895 (GRCm39)	missense	probably benign	0.00
R7509:Synpo	UTSW	18	60,736,566 (GRCm39)	missense	probably damaging	1.00
R7554:Synpo	UTSW	18	60,736,405 (GRCm39)	missense	probably benign	0.21
R7584:Synpo	UTSW	18	60,729,349 (GRCm39)	missense	probably damaging	0.96
R7615:Synpo	UTSW	18	60,737,547 (GRCm39)	missense	probably damaging	1.00
R7633:Synpo	UTSW	18	60,736,500 (GRCm39)	missense	probably damaging	1.00
R8499:Synpo	UTSW	18	60,736,044 (GRCm39)	missense	probably damaging	1.00
R8512:Synpo	UTSW	18	60,735,483 (GRCm39)	missense	probably damaging	0.99
R8996:Synpo	UTSW	18	60,737,230 (GRCm39)	missense	possibly damaging	0.95
R9116:Synpo	UTSW	18	60,735,599 (GRCm39)	missense	probably damaging	0.98
R9336:Synpo	UTSW	18	60,735,472 (GRCm39)	missense	probably damaging	0.96
R9798:Synpo	UTSW	18	60,736,832 (GRCm39)	missense	possibly damaging	0.81

Predicted Primers

PCR Primer
(F):5'- AAGACAGGCCCTGAGATGTG -3'
(R):5'- AGCAGCAGCCATACCAGATG -3'

Sequencing Primer
(F):5'- CCCTGAGATGTGTTACTTGAAGCAG -3'
(R):5'- ATACCAGATGCGGCCTTCC -3'

Posted On

2016-08-04