Mutagenetix > Incidental Mutation

Incidental Mutation 'R8345:Sec24a'

645182

Institutional Source

Beutler Lab

Gene Symbol

Sec24a

Ensembl Gene

ENSMUSG00000036391

Gene Name

SEC24 homolog A, COPII coat complex component

Synonyms

9430090N21Rik

MMRRC Submission

067801-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R8345 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

51583090-51649172 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 51634605 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Glutamine at position 107 (R107Q)

Ref Sequence

ENSEMBL: ENSMUSP00000104725 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000038210] [ENSMUST00000064297] [ENSMUST00000109092] [ENSMUST00000109097]

AlphaFold

Q3U2P1

Predicted Effect

probably benign
Transcript: ENSMUST00000038210
AA Change: R107Q

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000044370
Gene: ENSMUSG00000036391
AA Change: R107Q

Domain	Start	End	E-Value	Type
low complexity region	8	28	N/A	INTRINSIC
low complexity region	71	84	N/A	INTRINSIC
low complexity region	196	235	N/A	INTRINSIC
low complexity region	396	414	N/A	INTRINSIC
Pfam:zf-Sec23_Sec24	423	461	8e-19	PFAM
Pfam:Sec23_trunk	497	735	1.2e-87	PFAM
Pfam:Sec23_BS	740	824	1.1e-23	PFAM
Pfam:Sec23_helical	836	938	5.1e-27	PFAM
Pfam:Gelsolin	960	1035	7.2e-15	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000064297
AA Change: R107Q

PolyPhen 2 Score 0.063 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000068065
Gene: ENSMUSG00000036391
AA Change: R107Q

Domain	Start	End	E-Value	Type
low complexity region	8	28	N/A	INTRINSIC
low complexity region	71	84	N/A	INTRINSIC
low complexity region	196	235	N/A	INTRINSIC
low complexity region	396	414	N/A	INTRINSIC
Pfam:zf-Sec23_Sec24	424	462	3.5e-18	PFAM
Pfam:Sec23_trunk	498	589	1.3e-29	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000109092
AA Change: R107Q

PolyPhen 2 Score 0.037 (Sensitivity: 0.94; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000104720
Gene: ENSMUSG00000036391
AA Change: R107Q

Domain	Start	End	E-Value	Type
low complexity region	8	28	N/A	INTRINSIC
low complexity region	71	84	N/A	INTRINSIC
low complexity region	196	235	N/A	INTRINSIC
low complexity region	396	414	N/A	INTRINSIC
Pfam:zf-Sec23_Sec24	423	461	3.9e-19	PFAM
Pfam:Sec23_trunk	497	588	1.6e-30	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000109097
AA Change: R107Q

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000104725
Gene: ENSMUSG00000036391
AA Change: R107Q

Domain	Start	End	E-Value	Type
low complexity region	8	28	N/A	INTRINSIC
low complexity region	71	84	N/A	INTRINSIC
low complexity region	196	235	N/A	INTRINSIC
low complexity region	396	414	N/A	INTRINSIC
Pfam:zf-Sec23_Sec24	425	462	2.4e-16	PFAM
Pfam:Sec23_trunk	498	736	7.8e-87	PFAM
Pfam:Sec23_BS	741	825	1.1e-22	PFAM
Pfam:Sec23_helical	838	938	6.9e-28	PFAM
Pfam:Gelsolin	961	1036	9.3e-14	PFAM

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.5%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene belongs to a family of proteins that are homologous to yeast Sec24. This protein is a component of coat protein II (COPII)-coated vesicles that mediate protein transport from the endoplasmic reticulum. COPII acts in the cytoplasm to promote the transport of secretory, plasma membrane, and vacuolar proteins from the endoplasmic reticulum to the golgi complex. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
PHENOTYPE: Mice homozygous for a null allele exhibit decreased circulating cholesterol level, decreased circulating LDL cholesterol level, and abnormal liver physiology. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acsf3	T	C	8: 123,508,284 (GRCm39)	V260A	probably benign	Het
Adgrv1	T	C	13: 81,251,505 (GRCm39)	D6204G	probably damaging	Het
Ago3	T	A	4: 126,270,721 (GRCm39)	K258*	probably null	Het
Aspm	T	G	1: 139,392,011 (GRCm39)	Y787*	probably null	Het
Atp8b5	A	C	4: 43,291,714 (GRCm39)	D29A	probably benign	Het
Bdh2	A	T	3: 135,001,013 (GRCm39)	I128F	probably damaging	Het
Bmper	T	A	9: 23,136,126 (GRCm39)	M69K	probably benign	Het
Ccdc7a	C	T	8: 129,525,245 (GRCm39)	M1415I	probably benign	Het
Ccpg1	G	A	9: 72,913,001 (GRCm39)	R179H	probably damaging	Het
Cdc23	G	A	18: 34,767,150 (GRCm39)	T564I	probably benign	Het
Cemip	T	A	7: 83,591,373 (GRCm39)		probably null	Het
Cfap65	C	T	1: 74,967,203 (GRCm39)	G249R	probably benign	Het
Clec2m	T	A	6: 129,302,593 (GRCm39)	N145Y	probably damaging	Het
Cpsf1	T	A	15: 76,485,690 (GRCm39)	T435S	probably benign	Het
Dennd5a	T	C	7: 109,504,477 (GRCm39)	T879A	possibly damaging	Het
Diaph3	G	A	14: 87,066,529 (GRCm39)	Q955*	probably null	Het
Disp2	G	A	2: 118,641,284 (GRCm39)	V298M	unknown	Het
Dnah1	C	A	14: 30,986,551 (GRCm39)	D3671Y	probably damaging	Het
Dnmt3a	T	C	12: 3,885,234 (GRCm39)	S13P	unknown	Het
Eci3	G	A	13: 35,132,164 (GRCm39)	T228I	probably damaging	Het
Ecm2	T	C	13: 49,674,276 (GRCm39)	L232P	probably benign	Het
Ednra	G	A	8: 78,415,813 (GRCm39)	R145C	probably damaging	Het
Faap100	G	T	11: 120,267,856 (GRCm39)	H306N	possibly damaging	Het
Fam8a1	T	A	13: 46,827,054 (GRCm39)	I275K	probably damaging	Het
Fat3	C	A	9: 15,910,570 (GRCm39)	V1811L	probably benign	Het
Fbn2	C	T	18: 58,191,503 (GRCm39)	C1540Y	probably damaging	Het
Fcgbpl1	G	A	7: 27,854,785 (GRCm39)	V1804M	probably damaging	Het
Ffar3	A	G	7: 30,554,789 (GRCm39)	L177P	probably damaging	Het
Fmnl1	A	G	11: 103,077,440 (GRCm39)	T267A	possibly damaging	Het
Fsip1	T	C	2: 118,070,952 (GRCm39)	E246G	probably damaging	Het
Gemin4	A	G	11: 76,101,605 (GRCm39)	L1052P	probably damaging	Het
Gp2	C	T	7: 119,042,010 (GRCm39)	C505Y	probably benign	Het
Grm5	A	T	7: 87,723,746 (GRCm39)	I679F	probably damaging	Het
Hapln1	A	T	13: 89,732,902 (GRCm39)	D21V	probably benign	Het
Jak2	T	C	19: 29,262,270 (GRCm39)	S364P	probably damaging	Het
Kansl3	A	G	1: 36,387,897 (GRCm39)		probably null	Het
Kntc1	T	C	5: 123,924,993 (GRCm39)	L1102S	probably benign	Het
Mbd3l2	A	G	9: 18,355,779 (GRCm39)	I35V	probably benign	Het
Mdfic	G	T	6: 15,799,653 (GRCm39)	C260F	probably damaging	Het
Mroh2b	T	C	15: 4,973,808 (GRCm39)	S1109P	probably benign	Het
Myocd	A	T	11: 65,077,958 (GRCm39)	C612*	probably null	Het
Or4b13	A	T	2: 90,082,561 (GRCm39)	M257K	possibly damaging	Het
Or4c102	A	G	2: 88,422,435 (GRCm39)	M96V	probably benign	Het
Or4f17-ps1	T	A	2: 111,357,864 (GRCm39)	C86*	probably null	Het
Or52h7	T	A	7: 104,213,431 (GRCm39)	M1K	probably null	Het
Or5w22	A	T	2: 87,362,691 (GRCm39)	T105S	probably benign	Het
Or8k21	A	T	2: 86,145,451 (GRCm39)	Y60N	probably damaging	Het
Pard3	C	T	8: 128,050,549 (GRCm39)	R204W	probably damaging	Het
Per1	T	A	11: 68,998,382 (GRCm39)	N1031K	possibly damaging	Het
Plekhh3	A	G	11: 101,055,105 (GRCm39)	S583P	unknown	Het
Pramel12	C	T	4: 143,143,438 (GRCm39)	T68I	probably benign	Het
Prex2	T	A	1: 11,270,118 (GRCm39)	C1268S	possibly damaging	Het
Prpf6	T	C	2: 181,291,951 (GRCm39)	I756T	probably benign	Het
Pum2	T	C	12: 8,759,454 (GRCm39)	V98A	probably damaging	Het
Rad50	A	T	11: 53,574,968 (GRCm39)	S652T	probably benign	Het
Rfng	G	T	11: 120,674,901 (GRCm39)	P30T	unknown	Het
Rfx7	T	C	9: 72,524,973 (GRCm39)	I721T	probably benign	Het
Rpf1	G	T	3: 146,213,431 (GRCm39)	T240K	probably benign	Het
Ryr3	T	C	2: 112,483,270 (GRCm39)	N4189S	probably benign	Het
Samd15	G	C	12: 87,248,212 (GRCm39)	R299T	probably benign	Het
Scn3a	A	G	2: 65,329,335 (GRCm39)	M765T	possibly damaging	Het
Scn9a	G	A	2: 66,324,966 (GRCm39)	S1396L	probably damaging	Het
Sema4b	T	A	7: 79,870,567 (GRCm39)	V505E	probably damaging	Het
Siglec1	T	A	2: 130,920,498 (GRCm39)	T769S	possibly damaging	Het
Sit1	T	C	4: 43,483,168 (GRCm39)	E69G	possibly damaging	Het
Slc12a8	C	A	16: 33,371,321 (GRCm39)	D121E	probably benign	Het
Slc30a10	A	T	1: 185,187,664 (GRCm39)	Q135L	probably benign	Het
Suox	A	G	10: 128,507,200 (GRCm39)	V276A	probably benign	Het
Tbc1d9b	A	G	11: 50,040,659 (GRCm39)	D392G	probably damaging	Het
Tmed5	A	G	5: 108,273,823 (GRCm39)	W139R	probably damaging	Het
Tnks1bp1	C	T	2: 84,893,226 (GRCm39)	T389I	possibly damaging	Het
Vmn1r65	A	T	7: 6,011,256 (GRCm39)	I326K	probably benign	Het
Vmn2r43	A	G	7: 8,256,601 (GRCm39)	S421P	possibly damaging	Het
Vmn2r57	A	T	7: 41,076,968 (GRCm39)	N399K	possibly damaging	Het
Vmn2r90	T	A	17: 17,933,127 (GRCm39)	L229*	probably null	Het
Vwf	A	T	6: 125,656,265 (GRCm39)	D2610V		Het
Zfp646	C	T	7: 127,483,082 (GRCm39)	S1753L	probably benign	Het
Zfy2	C	A	Y: 2,107,096 (GRCm39)	V513F	possibly damaging	Het
Zranb2	A	T	3: 157,251,731 (GRCm39)	I317F	unknown	Het

Other mutations in Sec24a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00571:Sec24a	APN	11	51,627,331 (GRCm39)	nonsense	probably null
IGL00973:Sec24a	APN	11	51,620,404 (GRCm39)	critical splice acceptor site	probably null
IGL01364:Sec24a	APN	11	51,604,356 (GRCm39)	critical splice donor site	probably null
IGL01476:Sec24a	APN	11	51,599,783 (GRCm39)	missense	possibly damaging	0.88
IGL01725:Sec24a	APN	11	51,614,405 (GRCm39)	splice site	probably null
IGL02069:Sec24a	APN	11	51,624,761 (GRCm39)	splice site	probably benign
IGL02230:Sec24a	APN	11	51,599,861 (GRCm39)	missense	possibly damaging	0.88
IGL02617:Sec24a	APN	11	51,603,014 (GRCm39)	critical splice donor site	probably null
IGL02655:Sec24a	APN	11	51,625,482 (GRCm39)	missense	probably benign	0.43
IGL02756:Sec24a	APN	11	51,587,560 (GRCm39)	missense	probably benign	0.02
IGL03396:Sec24a	APN	11	51,599,794 (GRCm39)	missense	probably benign	0.17
R0153:Sec24a	UTSW	11	51,591,653 (GRCm39)	missense	probably benign	0.08
R0506:Sec24a	UTSW	11	51,634,622 (GRCm39)	missense	probably benign	0.03
R0625:Sec24a	UTSW	11	51,620,281 (GRCm39)	missense	probably damaging	0.98
R1084:Sec24a	UTSW	11	51,604,408 (GRCm39)	missense	probably damaging	1.00
R1166:Sec24a	UTSW	11	51,624,294 (GRCm39)	missense	possibly damaging	0.72
R1376:Sec24a	UTSW	11	51,591,740 (GRCm39)	splice site	probably benign
R1487:Sec24a	UTSW	11	51,622,713 (GRCm39)	missense	possibly damaging	0.92
R1541:Sec24a	UTSW	11	51,634,623 (GRCm39)	missense	probably benign	0.41
R1582:Sec24a	UTSW	11	51,599,794 (GRCm39)	missense	probably benign	0.17
R1643:Sec24a	UTSW	11	51,595,212 (GRCm39)	missense	probably benign	0.03
R1672:Sec24a	UTSW	11	51,634,775 (GRCm39)	nonsense	probably null
R1681:Sec24a	UTSW	11	51,586,016 (GRCm39)	missense	probably damaging	0.98
R1756:Sec24a	UTSW	11	51,624,590 (GRCm39)	splice site	probably benign
R1992:Sec24a	UTSW	11	51,627,190 (GRCm39)	missense	probably benign	0.00
R2159:Sec24a	UTSW	11	51,603,177 (GRCm39)	missense	probably damaging	1.00
R2177:Sec24a	UTSW	11	51,595,228 (GRCm39)	missense	probably benign	0.00
R2188:Sec24a	UTSW	11	51,614,411 (GRCm39)	missense	probably damaging	0.99
R2271:Sec24a	UTSW	11	51,607,277 (GRCm39)	missense	possibly damaging	0.91
R3414:Sec24a	UTSW	11	51,620,285 (GRCm39)	missense	probably damaging	1.00
R4349:Sec24a	UTSW	11	51,605,976 (GRCm39)	missense	probably benign	0.03
R4396:Sec24a	UTSW	11	51,605,991 (GRCm39)	missense	possibly damaging	0.86
R4629:Sec24a	UTSW	11	51,612,640 (GRCm39)	critical splice donor site	probably null
R5061:Sec24a	UTSW	11	51,604,359 (GRCm39)	splice site	probably null
R5577:Sec24a	UTSW	11	51,625,448 (GRCm39)	missense	probably benign	0.06
R5717:Sec24a	UTSW	11	51,598,037 (GRCm39)	missense	probably benign
R5915:Sec24a	UTSW	11	51,646,964 (GRCm39)	missense	probably benign	0.11
R6175:Sec24a	UTSW	11	51,622,718 (GRCm39)	missense	probably damaging	1.00
R6341:Sec24a	UTSW	11	51,608,603 (GRCm39)	missense	probably damaging	0.99
R6461:Sec24a	UTSW	11	51,604,373 (GRCm39)	missense	possibly damaging	0.76
R6610:Sec24a	UTSW	11	51,587,483 (GRCm39)	missense	probably benign
R6632:Sec24a	UTSW	11	51,604,476 (GRCm39)	nonsense	probably null
R6907:Sec24a	UTSW	11	51,603,103 (GRCm39)	missense	probably damaging	1.00
R6969:Sec24a	UTSW	11	51,591,643 (GRCm39)	missense	probably benign	0.35
R7132:Sec24a	UTSW	11	51,605,963 (GRCm39)	nonsense	probably null
R7274:Sec24a	UTSW	11	51,598,082 (GRCm39)	missense	probably damaging	1.00
R7475:Sec24a	UTSW	11	51,604,379 (GRCm39)	missense	probably damaging	1.00
R7699:Sec24a	UTSW	11	51,603,084 (GRCm39)	missense	probably damaging	1.00
R7700:Sec24a	UTSW	11	51,603,084 (GRCm39)	missense	probably damaging	1.00
R7935:Sec24a	UTSW	11	51,612,749 (GRCm39)	missense	probably benign	0.25
R8042:Sec24a	UTSW	11	51,595,144 (GRCm39)	missense	probably benign
R9217:Sec24a	UTSW	11	51,617,331 (GRCm39)	missense	probably benign	0.14
R9501:Sec24a	UTSW	11	51,603,122 (GRCm39)	missense	probably damaging	1.00
X0025:Sec24a	UTSW	11	51,620,374 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- GTTTGAAGTGCAGGGTCTCCAG -3'
(R):5'- GGCTATGATTCGCAACCTCC -3'

Sequencing Primer
(F):5'- CCGCTGTTAAATTTGGATTCCCAGG -3'
(R):5'- TATGATTCGCAACCTCCAGGATC -3'

Posted On

2020-09-02