Mutagenetix > Incidental Mutation

Incidental Mutation 'R5770:Sec16a'

446473

Institutional Source

Beutler Lab

Gene Symbol

Sec16a

Ensembl Gene

ENSMUSG00000026924

Gene Name

SEC16 homolog A, endoplasmic reticulum export factor

Synonyms

C230052J16Rik

MMRRC Submission

043370-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.959) question?

Stock #

R5770 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

26299443-26335228 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 26304402 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 2303 (D2303G)

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: D2303G

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000088796
Gene: ENSMUSG00000026924
AA Change: D2303G

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

possibly damaging
Transcript: ENSMUST00000114082
AA Change: D2303G

PolyPhen 2 Score 0.889 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000109716
Gene: ENSMUSG00000026924
AA Change: D2303G

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

noncoding transcript
Transcript: ENSMUST00000149010

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154486

Predicted Effect

unknown
Transcript: ENSMUST00000156442
AA Change: D852G

SMART Domains

Protein: ENSMUSP00000122255
Gene: ENSMUSG00000026924
AA Change: D852G

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: 98.8%
10x: 97.5%
20x: 95.9%

Validation Efficiency

93% (64/69)

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: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700030C10Rik	T	C	12: 20,865,460 (GRCm39)		noncoding transcript	Het
Abhd8	A	G	8: 71,909,972 (GRCm39)	V392A	probably benign	Het
Alpk3	A	G	7: 80,728,310 (GRCm39)	E480G	probably benign	Het
Ankfy1	C	G	11: 72,651,082 (GRCm39)	H1011D	probably damaging	Het
Aoc3	T	G	11: 101,222,578 (GRCm39)	Y271*	probably null	Het
Bcl9	T	C	3: 97,122,491 (GRCm39)	I103V	probably benign	Het
Cgnl1	C	T	9: 71,552,769 (GRCm39)		probably null	Het
Cyp2c23	T	A	19: 44,010,018 (GRCm39)	D109V	probably damaging	Het
Cyp2j13	A	T	4: 95,965,669 (GRCm39)	W13R	probably benign	Het
D630003M21Rik	T	C	2: 158,037,500 (GRCm39)		probably benign	Het
Desi2	A	T	1: 178,084,061 (GRCm39)		probably benign	Het
Dll3	T	C	7: 27,998,434 (GRCm39)	E177G	possibly damaging	Het
Ern2	C	T	7: 121,779,130 (GRCm39)	G238D	possibly damaging	Het
Gm11595	G	A	11: 99,663,381 (GRCm39)	R100C	unknown	Het
Gm6133	A	G	18: 78,393,464 (GRCm39)	K153E	probably benign	Het
Gpr68	A	T	12: 100,845,080 (GRCm39)	Y155N	probably benign	Het
Hcrtr2	T	A	9: 76,166,948 (GRCm39)	I130F	probably damaging	Het
Hk1	T	C	10: 62,122,228 (GRCm39)	K489R	probably benign	Het
Ints13	T	C	6: 146,456,571 (GRCm39)	N425S	probably damaging	Het
Itpkc	T	C	7: 26,912,413 (GRCm39)	D578G	probably damaging	Het
Kcns3	A	G	12: 11,142,250 (GRCm39)	S150P	probably benign	Het
Khdrbs3	T	A	15: 68,921,312 (GRCm39)		probably null	Het
Kif11	A	G	19: 37,379,313 (GRCm39)	I335V	probably benign	Het
Lrrn4	C	G	2: 132,714,076 (GRCm39)	C290S	probably damaging	Het
Macrod2	T	C	2: 141,074,102 (GRCm39)		probably benign	Het
Mgam	A	G	6: 40,646,738 (GRCm39)	N688S	probably benign	Het
Myh8	G	A	11: 67,188,026 (GRCm39)	E933K	probably damaging	Het
Nat8f5	T	C	6: 85,794,657 (GRCm39)	Y101C	probably damaging	Het
Nhlrc1	A	G	13: 47,168,188 (GRCm39)	V23A	probably benign	Het
Nkx2-3	T	A	19: 43,602,972 (GRCm39)	F193I	probably damaging	Het
Nlrp4b	T	A	7: 10,449,414 (GRCm39)	V172E	probably benign	Het
Nmrk1	G	T	19: 18,622,438 (GRCm39)	R172S	probably benign	Het
Nudcd3	T	C	11: 6,063,286 (GRCm39)	D201G	probably damaging	Het
Oprm1	G	A	10: 6,739,026 (GRCm39)	G51D	probably damaging	Het
Or10g9b	C	T	9: 39,917,634 (GRCm39)	V204I	probably benign	Het
Or13a18	A	G	7: 140,190,856 (GRCm39)	Y259C	probably damaging	Het
Or2t44	G	A	11: 58,677,420 (GRCm39)	R120H	probably benign	Het
Or2y14	A	G	11: 49,405,419 (GRCm39)	E318G	unknown	Het
Or4c12b	T	A	2: 89,646,893 (GRCm39)	D68E	probably damaging	Het
Or56a3	A	T	7: 104,740,102 (GRCm39)	I248N	probably damaging	Het
Or5ac23	A	T	16: 59,149,514 (GRCm39)	Y119*	probably null	Het
Pcdh15	T	A	10: 74,021,177 (GRCm39)	Y130*	probably null	Het
Pcdh9	G	A	14: 94,124,379 (GRCm39)	T597I	probably damaging	Het
Pcdhb19	A	G	18: 37,631,090 (GRCm39)	N295S	possibly damaging	Het
Pcnx3	T	C	19: 5,731,607 (GRCm39)		probably benign	Het
Pdzph1	A	T	17: 59,186,146 (GRCm39)	I1215N	probably damaging	Het
Phf21a	C	T	2: 92,182,199 (GRCm39)	T405I	possibly damaging	Het
Pkd1l2	C	A	8: 117,781,757 (GRCm39)	G763W	probably damaging	Het
Prox2	A	G	12: 85,134,154 (GRCm39)	F591L	probably benign	Het
Robo3	T	A	9: 37,330,497 (GRCm39)	H1033L	possibly damaging	Het
Sdha	A	T	13: 74,471,239 (GRCm39)	C222*	probably null	Het
Shoc1	T	C	4: 59,092,466 (GRCm39)	I238M	probably benign	Het
Slc16a5	A	G	11: 115,363,604 (GRCm39)	K422E	possibly damaging	Het
Slc22a30	A	T	19: 8,363,891 (GRCm39)	M232K	probably damaging	Het
Slc35b3	A	T	13: 39,121,734 (GRCm39)	F300I	probably damaging	Het
Spata2l	A	G	8: 123,962,459 (GRCm39)	V34A	probably damaging	Het
Susd2	C	T	10: 75,473,853 (GRCm39)	A581T	probably damaging	Het
Tecta	T	A	9: 42,256,885 (GRCm39)	Q1597L	possibly damaging	Het
Tgfb1i1	A	T	7: 127,847,719 (GRCm39)		probably benign	Het
Ticam1	TCACACA	TCACA	17: 56,577,629 (GRCm39)		probably null	Het
Tpm3-rs7	A	G	14: 113,552,807 (GRCm39)	T234A	probably benign	Het
Usp20	A	G	2: 30,907,520 (GRCm39)	Y684C	probably damaging	Het
Zc3h4	T	A	7: 16,163,536 (GRCm39)	M585K	unknown	Het
Zfp292	A	G	4: 34,806,747 (GRCm39)	I2099T	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
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
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
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'- ACTGAGCTGGCTGAATCACC -3'
(R):5'- CAGAACTACCAGGCATATCAGAGTAG -3'

Sequencing Primer
(F):5'- TGGCTGAATCACCATTCCAGG -3'
(R):5'- CCAGGCATATCAGAGTAGTGTTTAG -3'

Posted On

2016-11-21