Mutagenetix > Incidental Mutation

Incidental Mutation 'R1524:Sec16a'

167692

Institutional Source

Beutler Lab

Gene Symbol

Sec16a

Ensembl Gene

ENSMUSG00000026924

Gene Name

SEC16 homolog A, endoplasmic reticulum export factor

Synonyms

C230052J16Rik

MMRRC Submission

039565-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.961) question?

Stock #

R1524 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

26299443-26335228 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 26318394 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Phenylalanine at position 1566 (V1566F)

Ref Sequence

ENSEMBL: ENSMUSP00000088796 (fasta)

Gene Model

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

AlphaFold

E9QAT4

Predicted Effect

probably damaging
Transcript: ENSMUST00000091252
AA Change: V1566F

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

SMART Domains

Protein: ENSMUSP00000088796
Gene: ENSMUSG00000026924
AA Change: V1566F

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 damaging
Transcript: ENSMUST00000114082
AA Change: V1566F

PolyPhen 2 Score 0.973 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000109716
Gene: ENSMUSG00000026924
AA Change: V1566F

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

unknown
Transcript: ENSMUST00000156442
AA Change: V115F

SMART Domains

Protein: ENSMUSP00000122255
Gene: ENSMUSG00000026924
AA Change: V115F

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

0.6467

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.3%
20x: 95.5%

Validation Efficiency

97% (68/70)

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310003L06Rik	G	T	5: 88,119,548 (GRCm39)	V102L	probably benign	Het
Adck1	T	C	12: 88,368,854 (GRCm39)	Y111H	probably damaging	Het
Adcy10	G	T	1: 165,345,972 (GRCm39)	K340N	probably damaging	Het
Aebp1	T	C	11: 5,820,089 (GRCm39)	V355A	probably damaging	Het
Atp2b2	T	C	6: 113,751,162 (GRCm39)		probably benign	Het
Atrn	T	C	2: 130,799,000 (GRCm39)	V390A	probably benign	Het
Bpifc	T	A	10: 85,813,599 (GRCm39)	Q315L	probably benign	Het
C1qtnf6	T	G	15: 78,409,092 (GRCm39)		probably null	Het
Cab39l	A	G	14: 59,757,186 (GRCm39)		probably benign	Het
Capn12	T	A	7: 28,582,189 (GRCm39)		probably benign	Het
Ceacam18	A	C	7: 43,288,779 (GRCm39)	T177P	possibly damaging	Het
Ces5a	A	T	8: 94,252,293 (GRCm39)	F200I	probably damaging	Het
Cldn19	G	T	4: 119,114,248 (GRCm39)		probably null	Het
Cntnap2	A	G	6: 46,507,613 (GRCm39)	S46P	probably damaging	Het
Dchs1	A	G	7: 105,413,732 (GRCm39)	Y1028H	probably damaging	Het
Exd1	A	T	2: 119,355,155 (GRCm39)	F253L	probably damaging	Het
Fam161a	A	G	11: 22,965,826 (GRCm39)	N40D	possibly damaging	Het
Fam81a	A	T	9: 70,032,390 (GRCm39)	I34N	probably damaging	Het
Fchsd1	A	C	18: 38,098,950 (GRCm39)		probably null	Het
Fut11	T	A	14: 20,746,234 (GRCm39)	F359I	possibly damaging	Het
Fut7	T	C	2: 25,315,159 (GRCm39)	V92A	probably damaging	Het
Grid2	C	G	6: 64,406,738 (GRCm39)	F699L	possibly damaging	Het
Grin2a	A	G	16: 9,481,467 (GRCm39)	S445P	possibly damaging	Het
H2al2b	A	C	Y: 2,720,391 (GRCm39)	F95C	probably damaging	Het
Hecw2	T	C	1: 53,890,777 (GRCm39)	D1246G	probably damaging	Het
Ifit1	A	G	19: 34,625,032 (GRCm39)	N56S	probably damaging	Het
Ldb3	C	A	14: 34,277,313 (GRCm39)	V354L	probably benign	Het
Lrig2	T	C	3: 104,371,192 (GRCm39)	Y479C	probably benign	Het
Ltn1	A	G	16: 87,178,444 (GRCm39)	V1595A	probably damaging	Het
Macf1	A	G	4: 123,326,323 (GRCm39)	V2939A	possibly damaging	Het
Mapre3	T	G	5: 31,019,261 (GRCm39)	I35S	probably damaging	Het
Med16	A	T	10: 79,734,150 (GRCm39)	L588Q	probably damaging	Het
Ncapg2	T	C	12: 116,398,198 (GRCm39)		probably benign	Het
Ncstn	C	A	1: 171,899,716 (GRCm39)	R322L	possibly damaging	Het
Ndst1	A	T	18: 60,831,576 (GRCm39)	I594N	probably damaging	Het
Ndst3	A	G	3: 123,342,555 (GRCm39)	I752T	possibly damaging	Het
Obscn	G	T	11: 59,006,681 (GRCm39)	S1185R	probably damaging	Het
Or5b112	T	A	19: 13,319,486 (GRCm39)	C121*	probably null	Het
Or6aa1	A	G	7: 86,044,020 (GRCm39)	S229P	probably benign	Het
Or9q1	A	T	19: 13,805,679 (GRCm39)	L27H	probably damaging	Het
Otof	T	A	5: 30,536,900 (GRCm39)	D1285V	probably benign	Het
Pcnx2	A	G	8: 126,617,880 (GRCm39)	I125T	probably benign	Het
Pde4a	T	C	9: 21,112,543 (GRCm39)	S240P	probably damaging	Het
Pi15	T	C	1: 17,690,076 (GRCm39)	S126P	probably benign	Het
Pkhd1	T	C	1: 20,188,004 (GRCm39)	S3435G	probably damaging	Het
Plin1	C	A	7: 79,376,338 (GRCm39)	V133L	probably benign	Het
Pnpt1	T	A	11: 29,080,776 (GRCm39)	C7S	unknown	Het
Ppp3ca	A	T	3: 136,503,579 (GRCm39)	M51L	probably benign	Het
Primpol	G	T	8: 47,039,502 (GRCm39)		probably benign	Het
Prlr	T	C	15: 10,319,419 (GRCm39)	V116A	probably damaging	Het
Ptgr3	A	G	18: 84,112,831 (GRCm39)	E169G	probably benign	Het
Rnf139	A	G	15: 58,761,266 (GRCm39)	D35G	probably damaging	Het
Rsbn1l	T	A	5: 21,156,671 (GRCm39)	K38M	probably damaging	Het
Ryr3	T	A	2: 112,699,427 (GRCm39)	I888F	probably damaging	Het
Sin3b	A	G	8: 73,479,915 (GRCm39)	T874A	probably benign	Het
Skic3	T	A	13: 76,286,491 (GRCm39)	D891E	probably benign	Het
Slc5a5	A	C	8: 71,344,978 (GRCm39)	Y110D	probably damaging	Het
Smarcd2	C	T	11: 106,157,978 (GRCm39)	V97I	probably benign	Het
St6galnac2	G	A	11: 116,575,313 (GRCm39)		probably benign	Het
Tbc1d22b	T	C	17: 29,789,585 (GRCm39)	L149P	probably damaging	Het
Tekt2	T	C	4: 126,217,442 (GRCm39)	I208V	probably benign	Het
Tenm3	A	G	8: 48,682,016 (GRCm39)	I2522T	possibly damaging	Het
Ttll5	T	A	12: 85,911,342 (GRCm39)	Y233*	probably null	Het
Vcpip1	C	T	1: 9,794,727 (GRCm39)	E1215K	probably damaging	Het
Wdr4	T	C	17: 31,728,737 (GRCm39)		probably benign	Het
Zfp703	G	A	8: 27,469,401 (GRCm39)	G355D	probably damaging	Het
Zfp830	T	A	11: 82,655,794 (GRCm39)	D199E	probably damaging	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
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
R4293: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'- TTCTCTGAGCCAATCGACGGACAC -3'
(R):5'- CAGTATGTCCCTGCCCACATGAAG -3'

Sequencing Primer
(F):5'- TTCTTCCGGCCATACAGCAAG -3'
(R):5'- CTGCCCACATGAAGAGTCAGG -3'

Posted On

2014-04-13