Mutagenetix > Incidental Mutation

Incidental Mutation 'R1899:Scamp3'

214059

Institutional Source

Beutler Lab

Gene Symbol

Scamp3

Ensembl Gene

ENSMUSG00000028049

Gene Name

secretory carrier membrane protein 3

Synonyms

Sc3

MMRRC Submission

039919-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.938) question?

Stock #

R1899 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

89177473-89182765 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 89180260 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Aspartic acid at position 135 (N135D)

Ref Sequence

ENSEMBL: ENSMUSP00000096540 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029684] [ENSMUST00000041913] [ENSMUST00000090927] [ENSMUST00000098941] [ENSMUST00000117278] [ENSMUST00000119707] [ENSMUST00000120697] [ENSMUST00000121212] [ENSMUST00000121931] [ENSMUST00000127982] [ENSMUST00000140473] [ENSMUST00000128318] [ENSMUST00000147696]

AlphaFold

O35609

Predicted Effect

probably damaging
Transcript: ENSMUST00000029684
AA Change: N135D

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

SMART Domains

Protein: ENSMUSP00000029684
Gene: ENSMUSG00000028049
AA Change: N135D

Domain	Start	End	E-Value	Type
low complexity region	49	69	N/A	INTRINSIC
coiled coil region	89	127	N/A	INTRINSIC
Pfam:SCAMP	133	310	1.5e-76	PFAM
low complexity region	329	348	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000041913

SMART Domains

Protein: ENSMUSP00000039261
Gene: ENSMUSG00000032657

Domain	Start	End	E-Value	Type
low complexity region	3	22	N/A	INTRINSIC
Pfam:CD20	36	196	8e-36	PFAM
low complexity region	243	254	N/A	INTRINSIC
low complexity region	390	408	N/A	INTRINSIC
low complexity region	445	463	N/A	INTRINSIC
low complexity region	471	490	N/A	INTRINSIC
low complexity region	628	649	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000090927

SMART Domains

Protein: ENSMUSP00000088445
Gene: ENSMUSG00000068917

Domain	Start	End	E-Value	Type
low complexity region	24	50	N/A	INTRINSIC
low complexity region	54	72	N/A	INTRINSIC
low complexity region	105	137	N/A	INTRINSIC
S_TKc	161	477	1.46e-75	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000098941
AA Change: N135D

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

SMART Domains

Protein: ENSMUSP00000096540
Gene: ENSMUSG00000028049
AA Change: N135D

Domain	Start	End	E-Value	Type
low complexity region	49	69	N/A	INTRINSIC
coiled coil region	89	127	N/A	INTRINSIC
Pfam:SCAMP	133	229	5.5e-46	PFAM
Pfam:SCAMP	227	276	2.2e-11	PFAM
low complexity region	295	314	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000117278

SMART Domains

Protein: ENSMUSP00000113706
Gene: ENSMUSG00000032657

Domain	Start	End	E-Value	Type
low complexity region	3	22	N/A	INTRINSIC
transmembrane domain	34	56	N/A	INTRINSIC
Pfam:CD20	74	177	7.3e-13	PFAM
low complexity region	224	235	N/A	INTRINSIC
low complexity region	371	389	N/A	INTRINSIC
low complexity region	426	444	N/A	INTRINSIC
low complexity region	452	471	N/A	INTRINSIC
low complexity region	609	630	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000119707

SMART Domains

Protein: ENSMUSP00000113579
Gene: ENSMUSG00000032657

Domain	Start	End	E-Value	Type
low complexity region	3	22	N/A	INTRINSIC
Pfam:CD20	36	196	1.9e-18	PFAM
low complexity region	312	330	N/A	INTRINSIC
low complexity region	367	385	N/A	INTRINSIC
low complexity region	393	412	N/A	INTRINSIC
low complexity region	550	571	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000120697
AA Change: N136D

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000112846
Gene: ENSMUSG00000028049
AA Change: N136D

Domain	Start	End	E-Value	Type
low complexity region	50	70	N/A	INTRINSIC
coiled coil region	90	128	N/A	INTRINSIC
Pfam:SCAMP	135	310	1.1e-67	PFAM
low complexity region	330	349	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000121212

SMART Domains

Protein: ENSMUSP00000113390
Gene: ENSMUSG00000068917

Domain	Start	End	E-Value	Type
low complexity region	24	50	N/A	INTRINSIC
low complexity region	54	73	N/A	INTRINSIC
low complexity region	106	138	N/A	INTRINSIC
S_TKc	162	478	1.46e-75	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000121931

SMART Domains

Protein: ENSMUSP00000113861
Gene: ENSMUSG00000068917

Domain	Start	End	E-Value	Type
low complexity region	24	50	N/A	INTRINSIC
low complexity region	54	73	N/A	INTRINSIC
low complexity region	106	142	N/A	INTRINSIC
S_TKc	163	479	1.46e-75	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124291

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126115

Predicted Effect

probably benign
Transcript: ENSMUST00000127982

SMART Domains

Protein: ENSMUSP00000114855
Gene: ENSMUSG00000032657

Domain	Start	End	E-Value	Type
low complexity region	3	22	N/A	INTRINSIC
Pfam:CD20	36	77	6.7e-9	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153255

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148881

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156447

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138822

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131146

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000129294

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132830

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139221

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000136165

Predicted Effect

probably benign
Transcript: ENSMUST00000140473

Predicted Effect

probably benign
Transcript: ENSMUST00000128318

SMART Domains

Protein: ENSMUSP00000115761
Gene: ENSMUSG00000068917

Domain	Start	End	E-Value	Type
low complexity region	24	50	N/A	INTRINSIC
low complexity region	54	73	N/A	INTRINSIC
low complexity region	103	133	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000147696

SMART Domains

Protein: ENSMUSP00000117185
Gene: ENSMUSG00000032657

Domain	Start	End	E-Value	Type
low complexity region	3	22	N/A	INTRINSIC
Pfam:CD20	36	196	1.9e-30	PFAM
low complexity region	242	253	N/A	INTRINSIC
low complexity region	324	349	N/A	INTRINSIC

Meta Mutation Damage Score

0.7453

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.6%
20x: 93.4%

Validation Efficiency

94% (94/100)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an integral membrane protein that belongs to the secretory carrier membrane protein family. The encoded protein functions as a carrier to the cell surface in post-golgi recycling pathways. This protein is also involved in protein trafficking in endosomal pathways. Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2011]

Allele List at MGI

Other mutations in this stock

Total: 98 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610009O20Rik	T	C	18: 38,258,342	W378R	probably benign	Het
4930522L14Rik	T	A	5: 109,736,798	Q398L	probably benign	Het
4930596D02Rik	T	G	14: 35,810,132	K162T	probably damaging	Het
Abca8b	G	T	11: 109,937,918	T1353K	possibly damaging	Het
Abcg3	A	C	5: 104,938,199	C565G	probably damaging	Het
Actr3b	G	A	5: 25,829,538	V185I	possibly damaging	Het
Akap6	A	T	12: 53,141,852	E2016D	possibly damaging	Het
Aldh3b2	T	C	19: 3,978,662	V148A	possibly damaging	Het
Ankfy1	C	T	11: 72,754,407	Q771*	probably null	Het
Anks1b	A	G	10: 90,260,756	D425G	probably damaging	Het
Arrb1	T	C	7: 99,582,297		probably benign	Het
Atg2a	C	A	19: 6,245,067	T170N	probably damaging	Het
Atp8b5	C	T	4: 43,361,804	R617C	possibly damaging	Het
Bicra	T	C	7: 15,987,751	T614A	possibly damaging	Het
Cacna1i	A	G	15: 80,391,642	D167G	possibly damaging	Het
Calr4	T	G	4: 109,246,293		probably null	Het
Camsap3	G	T	8: 3,603,922	E515*	probably null	Het
Casp8ap2	T	C	4: 32,643,647	S907P	probably damaging	Het
Cdk19	T	A	10: 40,479,780		probably benign	Het
Chst14	A	G	2: 118,927,015	M122V	possibly damaging	Het
Cntn4	A	G	6: 106,675,813	M748V	probably benign	Het
Col7a1	A	G	9: 108,978,888	D2552G	unknown	Het
Cpeb2	C	A	5: 43,277,587	P600Q	probably damaging	Het
Cyp2a5	C	T	7: 26,839,033	R274*	probably null	Het
Dexi	A	G	16: 10,542,518	F58S	probably damaging	Het
Dlg5	C	A	14: 24,148,300	G1522W	probably damaging	Het
Dock2	T	C	11: 34,294,286	H1048R	probably benign	Het
Dpp4	T	C	2: 62,345,050		probably benign	Het
Dusp10	A	T	1: 184,069,180	K381N	possibly damaging	Het
Ercc4	A	G	16: 13,147,787	E761G	probably damaging	Het
Ern2	T	C	7: 122,183,842		probably benign	Het
Fam83f	A	T	15: 80,692,080	T311S	probably damaging	Het
Fat2	T	C	11: 55,262,178	D3736G	probably benign	Het
Fgf11	G	T	11: 69,801,453	T58K	probably benign	Het
Galntl5	C	G	5: 25,198,532	S167*	probably null	Het
Glg1	T	G	8: 111,165,674	E846D	probably benign	Het
Grm8	C	A	6: 28,125,895	E77D	probably damaging	Het
Hmcn1	A	T	1: 150,657,451	D3028E	probably damaging	Het
Htt	A	G	5: 34,907,085	I2943V	probably benign	Het
Ift80	T	C	3: 68,918,513	K498R	probably benign	Het
Ipo9	A	T	1: 135,400,146	M509K	probably damaging	Het
Kcnj3	T	C	2: 55,437,244	V15A	probably damaging	Het
Kcnn3	A	T	3: 89,520,455		probably benign	Het
Larp1b	T	A	3: 40,964,084	D53E	probably benign	Het
Ltf	T	C	9: 111,022,845	F117L	possibly damaging	Het
Maml1	A	G	11: 50,266,130	L406P	probably damaging	Het
Mnx1	G	A	5: 29,473,957	A376V	unknown	Het
Mroh2a	G	A	1: 88,235,376	R376H	probably benign	Het
Mrpl4	A	G	9: 21,006,831	Y111C	probably damaging	Het
Mto1	T	C	9: 78,461,517		probably benign	Het
Nalcn	A	T	14: 123,316,126	M972K	possibly damaging	Het
Nemf	T	C	12: 69,346,378	I225V	probably null	Het
Nipal4	T	G	11: 46,150,231	D379A	probably damaging	Het
Nktr	A	G	9: 121,748,866		probably benign	Het
Nlrp5	A	G	7: 23,404,797	T28A	probably benign	Het
Nxph1	T	A	6: 9,247,622	Y198N	probably damaging	Het
Olfr1037	A	T	2: 86,085,720	V19D	probably benign	Het
Olfr1230	T	C	2: 89,296,670	N200S	probably damaging	Het
Olfr1436	T	C	19: 12,298,343	Y263C	probably damaging	Het
P2rx7	A	G	5: 122,673,736	Y370C	probably benign	Het
Piezo1	T	C	8: 122,482,645		probably benign	Het
Piezo1	T	C	8: 122,489,566	D1401G	probably damaging	Het
Plxnd1	A	G	6: 115,969,363	L879P	probably benign	Het
Polr2a	A	T	11: 69,743,946	I636N	probably damaging	Het
Prex2	G	T	1: 11,162,366	E886*	probably null	Het
Proca1	A	T	11: 78,205,021	I73F	probably damaging	Het
Prss55	A	T	14: 64,079,390	V101E	probably benign	Het
Psg26	T	A	7: 18,478,425	H335L	probably benign	Het
Rai1	A	G	11: 60,185,920	E270G	probably benign	Het
Reep1	A	G	6: 71,780,797	N127D	probably benign	Het
Rims1	G	T	1: 22,428,474	P769Q	probably damaging	Het
Robo4	A	T	9: 37,404,070		probably benign	Het
Ryr2	A	T	13: 11,591,336	D888E	probably benign	Het
Sdk2	C	T	11: 113,838,646		silent	Het
Sema4f	A	G	6: 82,918,029	M395T	probably benign	Het
Sgip1	T	C	4: 102,968,337		probably null	Het
Sik2	A	T	9: 50,995,674		probably benign	Het
Smtn	G	T	11: 3,531,326	A223D	possibly damaging	Het
Spen	T	C	4: 141,470,343	T3405A	probably benign	Het
Srebf1	A	G	11: 60,203,486	L601P	probably damaging	Het
Srsf11	A	T	3: 158,031,580		probably benign	Het
Tacc2	T	G	7: 130,624,202	S891R	possibly damaging	Het
Tbc1d17	T	A	7: 44,841,633		probably benign	Het
Tgfbr3l	C	A	8: 4,249,600	R128S	probably damaging	Het
Thsd1	G	A	8: 22,252,318		probably benign	Het
Tlx3	T	C	11: 33,203,072	S130G	probably benign	Het
Tmem25	A	T	9: 44,798,216		probably null	Het
Trak2	A	T	1: 58,946,336	M1K	probably null	Het
Trappc12	C	T	12: 28,746,985	E183K	probably damaging	Het
Ubl3	A	G	5: 148,509,280	V71A	possibly damaging	Het
Unc50	A	G	1: 37,438,799	Y254C	probably damaging	Het
Unkl	T	C	17: 25,229,460		probably null	Het
Uso1	T	A	5: 92,201,192	S819T	probably benign	Het
Yes1	A	T	5: 32,645,051	R103S	probably damaging	Het
Zfp131	A	G	13: 119,767,025	V396A	probably damaging	Het
Zfp553	T	C	7: 127,235,654	I127T	possibly damaging	Het
Zfp599	A	T	9: 22,251,549	N102K	probably benign	Het
Zmynd10	A	T	9: 107,550,037	Q288L	probably benign	Het

Other mutations in Scamp3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01063:Scamp3	APN	3	89177666	unclassified	probably benign
IGL01362:Scamp3	APN	3	89179134	missense	probably benign	0.01
IGL02269:Scamp3	APN	3	89180734	missense	probably benign	0.12
R0908:Scamp3	UTSW	3	89179439	splice site	probably null
R1160:Scamp3	UTSW	3	89181198	missense	probably damaging	1.00
R4237:Scamp3	UTSW	3	89181927	splice site	probably null
R4238:Scamp3	UTSW	3	89181927	splice site	probably null
R4373:Scamp3	UTSW	3	89181927	splice site	probably null
R4374:Scamp3	UTSW	3	89181927	splice site	probably null
R5013:Scamp3	UTSW	3	89180909	unclassified	probably benign
R5023:Scamp3	UTSW	3	89182293	unclassified	probably benign
R5057:Scamp3	UTSW	3	89182293	unclassified	probably benign
R5522:Scamp3	UTSW	3	89177622	missense	possibly damaging	0.90
R5762:Scamp3	UTSW	3	89181197	missense	probably damaging	1.00
R6788:Scamp3	UTSW	3	89181949	missense	probably benign	0.00
R7586:Scamp3	UTSW	3	89180366	missense	probably damaging	1.00
R7606:Scamp3	UTSW	3	89181218	missense	probably damaging	1.00
R7769:Scamp3	UTSW	3	89177991	missense	probably damaging	1.00
R8412:Scamp3	UTSW	3	89181218	missense	probably damaging	1.00
R9680:Scamp3	UTSW	3	89180254	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- GGAGCCTCAGATGTTTCGAG -3'
(R):5'- AAGTGTCTTGCTCTCAGAGTTG -3'

Sequencing Primer
(F):5'- GAGCCTCAGATGTTTCGAGTAGTAAC -3'
(R):5'- TGTGGGGCATTTAATAGATTAATCTG -3'

Posted On

2014-07-14