Mutagenetix > Incidental Mutation

Incidental Mutation 'R4293:Sec16a'

323151

Institutional Source

Beutler Lab

Gene Symbol

Sec16a

Ensembl Gene

ENSMUSG00000026924

Gene Name

SEC16 homolog A, endoplasmic reticulum export factor

Synonyms

C230052J16Rik

MMRRC Submission

041082-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.961) question?

Stock #

R4293 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

26299443-26335228 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 26312167 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 1998 (Y1998H)

Ref Sequence

ENSEMBL: ENSMUSP00000088796 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000091252] [ENSMUST00000114082]

AlphaFold

E9QAT4

Predicted Effect

probably benign
Transcript: ENSMUST00000091252
AA Change: Y1998H

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000088796
Gene: ENSMUSG00000026924
AA Change: Y1998H

Domain	Start	End	E-Value	Type
low complexity region	2	21	N/A	INTRINSIC
low complexity region	204	221	N/A	INTRINSIC
low complexity region	243	254	N/A	INTRINSIC
low complexity region	371	382	N/A	INTRINSIC
low complexity region	537	561	N/A	INTRINSIC
low complexity region	608	621	N/A	INTRINSIC
low complexity region	760	777	N/A	INTRINSIC
low complexity region	1096	1105	N/A	INTRINSIC
low complexity region	1134	1150	N/A	INTRINSIC
low complexity region	1185	1195	N/A	INTRINSIC
low complexity region	1370	1392	N/A	INTRINSIC
Pfam:Sec16	1463	1565	3.1e-24	PFAM
low complexity region	1600	1614	N/A	INTRINSIC
Pfam:Sec16_C	1635	1898	2.3e-39	PFAM
low complexity region	2109	2124	N/A	INTRINSIC
low complexity region	2165	2177	N/A	INTRINSIC
low complexity region	2187	2197	N/A	INTRINSIC
low complexity region	2227	2242	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000114082
AA Change: Y1998H

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

SMART Domains

Protein: ENSMUSP00000109716
Gene: ENSMUSG00000026924
AA Change: Y1998H

Domain	Start	End	E-Value	Type
low complexity region	2	21	N/A	INTRINSIC
low complexity region	204	221	N/A	INTRINSIC
low complexity region	243	254	N/A	INTRINSIC
low complexity region	371	382	N/A	INTRINSIC
low complexity region	537	561	N/A	INTRINSIC
low complexity region	608	621	N/A	INTRINSIC
low complexity region	760	777	N/A	INTRINSIC
low complexity region	1096	1105	N/A	INTRINSIC
low complexity region	1134	1150	N/A	INTRINSIC
low complexity region	1185	1195	N/A	INTRINSIC
low complexity region	1370	1392	N/A	INTRINSIC
Pfam:Sec16	1464	1564	2.6e-10	PFAM
low complexity region	1600	1614	N/A	INTRINSIC
Pfam:Sec16_C	1636	1887	6.8e-45	PFAM
low complexity region	2109	2124	N/A	INTRINSIC
low complexity region	2165	2177	N/A	INTRINSIC
low complexity region	2187	2197	N/A	INTRINSIC
low complexity region	2227	2242	N/A	INTRINSIC
low complexity region	2310	2320	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148306

Predicted Effect

unknown
Transcript: ENSMUST00000156442
AA Change: Y547H

SMART Domains

Protein: ENSMUSP00000122255
Gene: ENSMUSG00000026924
AA Change: Y547H

Domain	Start	End	E-Value	Type
Pfam:Sec16	14	114	7.7e-11	PFAM
low complexity region	150	164	N/A	INTRINSIC
Pfam:Sec16_C	186	438	1.6e-45	PFAM
low complexity region	659	674	N/A	INTRINSIC
low complexity region	715	727	N/A	INTRINSIC
low complexity region	737	747	N/A	INTRINSIC
low complexity region	777	792	N/A	INTRINSIC

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.3%
3x: 98.8%
10x: 97.7%
20x: 96.2%

Validation Efficiency

98% (60/61)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that forms part of the Sec16 complex. This protein has a role in protein transport from the endoplasmic reticulum (ER) to the Golgi and mediates COPII vesicle formation at the transitional ER. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Feb 2013]

Allele List at MGI

Other mutations in this stock

Total: 48 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Actn3	T	C	19: 4,915,468 (GRCm39)	E428G	probably benign	Het
Arfgef2	T	C	2: 166,732,211 (GRCm39)	I1600T	probably benign	Het
Arid3b	A	T	9: 57,697,713 (GRCm39)		probably benign	Het
Asgr2	C	A	11: 69,989,057 (GRCm39)	T167K	probably benign	Het
Atf6b	T	A	17: 34,871,648 (GRCm39)	M428K	probably benign	Het
Atpaf1	A	T	4: 115,645,556 (GRCm39)	M142L	probably benign	Het
Bivm	A	T	1: 44,177,793 (GRCm39)	R364S	probably damaging	Het
Bms1	T	C	6: 118,382,308 (GRCm39)		probably null	Het
Brwd1	G	A	16: 95,818,804 (GRCm39)	P1343S	probably damaging	Het
Cdca2	T	C	14: 67,952,299 (GRCm39)	D24G	probably benign	Het
Celsr2	T	C	3: 108,300,993 (GRCm39)	R2767G	probably benign	Het
Cip2a	T	A	16: 48,833,612 (GRCm39)	F571Y	probably benign	Het
Cyp2c55	A	T	19: 39,000,235 (GRCm39)	I145F	probably damaging	Het
Ddx18	T	C	1: 121,489,121 (GRCm39)	T309A	probably benign	Het
Dlg3	A	T	X: 99,840,288 (GRCm39)		probably benign	Het
Fbf1	A	G	11: 116,039,720 (GRCm39)	L713P	probably damaging	Het
Fhdc1	C	A	3: 84,352,133 (GRCm39)	V1031F	probably benign	Het
Fnbp1	A	G	2: 30,995,362 (GRCm39)	F24S	probably damaging	Het
Gm16686	A	T	4: 88,673,710 (GRCm39)		probably benign	Het
Gmps	A	G	3: 63,898,040 (GRCm39)	M275V	probably damaging	Het
Igdcc4	A	G	9: 65,031,892 (GRCm39)		probably null	Het
Kcnv1	G	A	15: 44,977,840 (GRCm39)	T66M	probably damaging	Het
Kif18a	T	C	2: 109,123,398 (GRCm39)	V224A	probably benign	Het
Lbr	C	T	1: 181,648,267 (GRCm39)	C398Y	probably damaging	Het
Lmf1	T	C	17: 25,873,455 (GRCm39)	L320P	probably damaging	Het
Mapkapk3	T	C	9: 107,136,131 (GRCm39)		probably benign	Het
Mettl18	A	G	1: 163,824,171 (GRCm39)	D164G	probably damaging	Het
Myo5a	A	T	9: 75,051,453 (GRCm39)	T349S	probably benign	Het
Or1ad6	T	C	11: 50,860,253 (GRCm39)	M136T	probably damaging	Het
Or8d2b	A	G	9: 38,788,609 (GRCm39)	I46V	probably damaging	Het
Pcdhb5	T	A	18: 37,455,734 (GRCm39)	S705T	possibly damaging	Het
Phf14	C	T	6: 11,987,096 (GRCm39)	P559S	probably damaging	Het
Pik3c3	G	A	18: 30,477,043 (GRCm39)	A855T	probably damaging	Het
Plpp4	A	G	7: 128,909,356 (GRCm39)	E22G	probably damaging	Het
Rev1	A	T	1: 38,147,500 (GRCm39)	D13E	possibly damaging	Het
Slc4a5	C	T	6: 83,237,511 (GRCm39)	R165C	probably damaging	Het
Slfn10-ps	T	C	11: 82,926,260 (GRCm39)		noncoding transcript	Het
Slfn9	T	C	11: 82,873,334 (GRCm39)	N523S	probably benign	Het
Spata13	T	A	14: 60,947,004 (GRCm39)	M684K	probably damaging	Het
Srsf6	T	C	2: 162,776,636 (GRCm39)		probably benign	Het
Stk32c	T	C	7: 138,700,704 (GRCm39)		probably null	Het
Tenm3	T	C	8: 48,848,693 (GRCm39)	T49A	probably damaging	Het
Tep1	T	C	14: 51,084,318 (GRCm39)	I954V	probably benign	Het
Tmem237	A	G	1: 59,158,995 (GRCm39)		probably benign	Het
Vmn2r101	A	T	17: 19,832,303 (GRCm39)	R766S	probably damaging	Het
Vwce	A	G	19: 10,636,996 (GRCm39)	T693A	probably benign	Het
Xpr1	A	G	1: 155,188,542 (GRCm39)	F366S	possibly damaging	Het
Zfp317	A	G	9: 19,557,990 (GRCm39)		probably null	Het

Other mutations in Sec16a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00337:Sec16a	APN	2	26,329,499 (GRCm39)	missense	probably benign	0.15
IGL00435:Sec16a	APN	2	26,320,113 (GRCm39)	missense	probably benign	0.00
IGL00469:Sec16a	APN	2	26,318,312 (GRCm39)	missense	probably damaging	1.00
IGL01622:Sec16a	APN	2	26,328,915 (GRCm39)	missense	probably benign	0.00
IGL01623:Sec16a	APN	2	26,328,915 (GRCm39)	missense	probably benign	0.00
IGL02158:Sec16a	APN	2	26,306,644 (GRCm39)	critical splice donor site	probably null
IGL02188:Sec16a	APN	2	26,326,020 (GRCm39)	missense	probably damaging	1.00
IGL02445:Sec16a	APN	2	26,312,052 (GRCm39)	missense	probably benign
IGL02568:Sec16a	APN	2	26,326,054 (GRCm39)	missense	probably damaging	1.00
IGL02710:Sec16a	APN	2	26,320,142 (GRCm39)	missense	possibly damaging	0.75
IGL02735:Sec16a	APN	2	26,318,149 (GRCm39)	splice site	probably benign
IGL02964:Sec16a	APN	2	26,309,735 (GRCm39)	missense	probably benign	0.00
IGL03027:Sec16a	APN	2	26,313,601 (GRCm39)	missense	probably benign	0.13
IGL03073:Sec16a	APN	2	26,329,195 (GRCm39)	missense	probably benign	0.02
IGL03297:Sec16a	APN	2	26,329,202 (GRCm39)	missense	probably benign	0.05
IGL03339:Sec16a	APN	2	26,325,945 (GRCm39)	missense	probably benign
H8562:Sec16a	UTSW	2	26,331,517 (GRCm39)	missense	probably benign
IGL03050:Sec16a	UTSW	2	26,305,759 (GRCm39)	missense	probably damaging	1.00
PIT4486001:Sec16a	UTSW	2	26,315,785 (GRCm39)	missense
R0039:Sec16a	UTSW	2	26,313,926 (GRCm39)	missense	probably benign	0.03
R0095:Sec16a	UTSW	2	26,315,772 (GRCm39)	splice site	probably null
R0095:Sec16a	UTSW	2	26,315,772 (GRCm39)	splice site	probably null
R0189:Sec16a	UTSW	2	26,314,426 (GRCm39)	splice site	probably null
R0255:Sec16a	UTSW	2	26,321,198 (GRCm39)	missense	probably damaging	0.97
R0278:Sec16a	UTSW	2	26,318,328 (GRCm39)	missense	probably damaging	1.00
R0739:Sec16a	UTSW	2	26,331,063 (GRCm39)	missense	possibly damaging	0.94
R0743:Sec16a	UTSW	2	26,309,734 (GRCm39)	missense	possibly damaging	0.67
R1446:Sec16a	UTSW	2	26,313,579 (GRCm39)	missense	probably benign	0.00
R1466:Sec16a	UTSW	2	26,321,169 (GRCm39)	missense	probably damaging	0.98
R1466:Sec16a	UTSW	2	26,321,169 (GRCm39)	missense	probably damaging	0.98
R1501:Sec16a	UTSW	2	26,330,057 (GRCm39)	missense	probably benign	0.16
R1524:Sec16a	UTSW	2	26,318,394 (GRCm39)	missense	probably damaging	1.00
R1584:Sec16a	UTSW	2	26,321,169 (GRCm39)	missense	probably damaging	0.98
R1649:Sec16a	UTSW	2	26,315,536 (GRCm39)	missense	probably damaging	1.00
R1744:Sec16a	UTSW	2	26,329,198 (GRCm39)	missense	probably damaging	1.00
R1959:Sec16a	UTSW	2	26,320,144 (GRCm39)	missense	probably benign	0.00
R1973:Sec16a	UTSW	2	26,316,501 (GRCm39)	missense	probably damaging	1.00
R2005:Sec16a	UTSW	2	26,329,092 (GRCm39)	missense	probably benign	0.27
R2073:Sec16a	UTSW	2	26,330,251 (GRCm39)	missense	probably damaging	1.00
R2074:Sec16a	UTSW	2	26,330,251 (GRCm39)	missense	probably damaging	1.00
R2075:Sec16a	UTSW	2	26,330,251 (GRCm39)	missense	probably damaging	1.00
R2151:Sec16a	UTSW	2	26,303,757 (GRCm39)	intron	probably benign
R2472:Sec16a	UTSW	2	26,329,948 (GRCm39)	missense	probably damaging	1.00
R2512:Sec16a	UTSW	2	26,329,037 (GRCm39)	missense	probably benign	0.00
R2520:Sec16a	UTSW	2	26,331,368 (GRCm39)	nonsense	probably null
R2571:Sec16a	UTSW	2	26,329,343 (GRCm39)	missense	probably benign	0.08
R3105:Sec16a	UTSW	2	26,328,433 (GRCm39)	missense	probably benign	0.14
R3508:Sec16a	UTSW	2	26,315,862 (GRCm39)	missense	probably damaging	1.00
R3809:Sec16a	UTSW	2	26,331,825 (GRCm39)	missense	possibly damaging	0.71
R3912:Sec16a	UTSW	2	26,304,399 (GRCm39)	missense	probably damaging	0.97
R4292:Sec16a	UTSW	2	26,312,167 (GRCm39)	missense	probably benign	0.01
R4294:Sec16a	UTSW	2	26,312,167 (GRCm39)	missense	probably benign	0.01
R4576:Sec16a	UTSW	2	26,321,131 (GRCm39)	nonsense	probably null
R4611:Sec16a	UTSW	2	26,331,817 (GRCm39)	missense	probably benign	0.04
R4627:Sec16a	UTSW	2	26,321,080 (GRCm39)	splice site	probably null
R4627:Sec16a	UTSW	2	26,319,405 (GRCm39)	missense	probably damaging	1.00
R4662:Sec16a	UTSW	2	26,320,582 (GRCm39)	missense	probably damaging	1.00
R4665:Sec16a	UTSW	2	26,302,970 (GRCm39)	intron	probably benign
R4906:Sec16a	UTSW	2	26,331,979 (GRCm39)	unclassified	probably benign
R4967:Sec16a	UTSW	2	26,302,883 (GRCm39)	missense	probably benign	0.00
R4983:Sec16a	UTSW	2	26,329,531 (GRCm39)	missense	probably benign
R5033:Sec16a	UTSW	2	26,309,661 (GRCm39)	missense	probably benign	0.00
R5251:Sec16a	UTSW	2	26,329,357 (GRCm39)	missense	probably benign	0.00
R5391:Sec16a	UTSW	2	26,330,044 (GRCm39)	missense	possibly damaging	0.82
R5457:Sec16a	UTSW	2	26,330,280 (GRCm39)	missense	probably benign	0.01
R5530:Sec16a	UTSW	2	26,329,264 (GRCm39)	missense	probably benign	0.00
R5645:Sec16a	UTSW	2	26,329,907 (GRCm39)	missense	probably benign	0.01
R5661:Sec16a	UTSW	2	26,329,649 (GRCm39)	missense	probably benign	0.01
R5770:Sec16a	UTSW	2	26,304,402 (GRCm39)	missense	probably damaging	0.99
R5830:Sec16a	UTSW	2	26,330,853 (GRCm39)	missense	probably benign	0.15
R5866:Sec16a	UTSW	2	26,309,650 (GRCm39)	missense	probably benign	0.00
R5875:Sec16a	UTSW	2	26,323,379 (GRCm39)	missense	probably damaging	1.00
R5906:Sec16a	UTSW	2	26,328,843 (GRCm39)	missense	possibly damaging	0.63
R5922:Sec16a	UTSW	2	26,305,651 (GRCm39)	missense	probably benign	0.05
R6076:Sec16a	UTSW	2	26,313,954 (GRCm39)	missense	probably damaging	1.00
R6091:Sec16a	UTSW	2	26,316,482 (GRCm39)	missense	probably damaging	1.00
R6295:Sec16a	UTSW	2	26,318,253 (GRCm39)	missense	probably damaging	1.00
R6302:Sec16a	UTSW	2	26,315,817 (GRCm39)	missense	probably damaging	1.00
R6309:Sec16a	UTSW	2	26,328,583 (GRCm39)	missense	probably benign	0.00
R6459:Sec16a	UTSW	2	26,313,512 (GRCm39)	missense	probably benign	0.04
R6520:Sec16a	UTSW	2	26,316,118 (GRCm39)	missense	probably damaging	1.00
R6631:Sec16a	UTSW	2	26,329,969 (GRCm39)	missense	probably damaging	1.00
R6657:Sec16a	UTSW	2	26,315,876 (GRCm39)	nonsense	probably null
R6750:Sec16a	UTSW	2	26,330,030 (GRCm39)	missense	probably benign	0.00
R6852:Sec16a	UTSW	2	26,331,431 (GRCm39)	missense	probably damaging	0.99
R6860:Sec16a	UTSW	2	26,320,124 (GRCm39)	missense	probably damaging	1.00
R6967:Sec16a	UTSW	2	26,320,498 (GRCm39)	missense	probably damaging	1.00
R6968:Sec16a	UTSW	2	26,320,498 (GRCm39)	missense	probably damaging	1.00
R6970:Sec16a	UTSW	2	26,320,498 (GRCm39)	missense	probably damaging	1.00
R6991:Sec16a	UTSW	2	26,320,498 (GRCm39)	missense	probably damaging	1.00
R6993:Sec16a	UTSW	2	26,313,586 (GRCm39)	missense	probably damaging	0.99
R7009:Sec16a	UTSW	2	26,326,014 (GRCm39)	nonsense	probably null
R7057:Sec16a	UTSW	2	26,315,277 (GRCm39)	missense	probably damaging	1.00
R7186:Sec16a	UTSW	2	26,330,715 (GRCm39)	nonsense	probably null
R7227:Sec16a	UTSW	2	26,328,935 (GRCm39)	missense	probably benign	0.01
R7234:Sec16a	UTSW	2	26,329,780 (GRCm39)	missense	probably damaging	1.00
R7259:Sec16a	UTSW	2	26,331,604 (GRCm39)	missense	probably benign	0.00
R7326:Sec16a	UTSW	2	26,329,729 (GRCm39)	missense	unknown
R7371:Sec16a	UTSW	2	26,331,734 (GRCm39)	missense	probably benign
R7388:Sec16a	UTSW	2	26,318,376 (GRCm39)	missense
R7414:Sec16a	UTSW	2	26,313,643 (GRCm39)	missense
R7417:Sec16a	UTSW	2	26,311,409 (GRCm39)	missense
R7501:Sec16a	UTSW	2	26,331,863 (GRCm39)	missense	probably damaging	1.00
R7558:Sec16a	UTSW	2	26,329,746 (GRCm39)	missense
R7696:Sec16a	UTSW	2	26,305,645 (GRCm39)	critical splice donor site	probably null
R7981:Sec16a	UTSW	2	26,311,384 (GRCm39)	critical splice donor site	probably null
R8117:Sec16a	UTSW	2	26,331,441 (GRCm39)	missense	probably benign	0.00
R8131:Sec16a	UTSW	2	26,300,958 (GRCm39)	missense
R8163:Sec16a	UTSW	2	26,306,433 (GRCm39)	missense
R8825:Sec16a	UTSW	2	26,313,586 (GRCm39)	missense
R8855:Sec16a	UTSW	2	26,329,852 (GRCm39)	missense	probably benign	0.16
R9165:Sec16a	UTSW	2	26,313,645 (GRCm39)	missense
R9216:Sec16a	UTSW	2	26,304,401 (GRCm39)	missense
R9283:Sec16a	UTSW	2	26,313,904 (GRCm39)	missense
R9506:Sec16a	UTSW	2	26,319,384 (GRCm39)	critical splice donor site	probably null
R9581:Sec16a	UTSW	2	26,328,647 (GRCm39)	missense
R9772:Sec16a	UTSW	2	26,329,417 (GRCm39)	missense	possibly damaging	0.87
X0011:Sec16a	UTSW	2	26,305,655 (GRCm39)	missense	probably damaging	1.00
X0034:Sec16a	UTSW	2	26,306,709 (GRCm39)	missense	probably benign	0.07
X0062:Sec16a	UTSW	2	26,306,709 (GRCm39)	missense	probably benign	0.07
Z1088:Sec16a	UTSW	2	26,329,105 (GRCm39)	missense	probably damaging	0.99
Z1176:Sec16a	UTSW	2	26,328,760 (GRCm39)	missense
Z1177:Sec16a	UTSW	2	26,329,333 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- GCATGACCAATTAGCTCTGC -3'
(R):5'- TGTACAGAGCAGCTTATGTGC -3'

Sequencing Primer
(F):5'- ATGACCAATTAGCTCTGCTCTCAGG -3'
(R):5'- ACAGAGCAGCTTATGTGCTTATG -3'

Posted On

2015-06-20