Mutagenetix > Incidental Mutation

Incidental Mutation 'R0008:Sec24d'

58196

Institutional Source

Beutler Lab

Gene Symbol

Sec24d

Ensembl Gene

ENSMUSG00000039234

Gene Name

SEC24 homolog D, COPII coat complex component

Synonyms

LOC383951, 2310020L09Rik

MMRRC Submission

038303-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0008 (G1)

Quality Score

108

Status

Validated

Chromosome

Chromosomal Location

123061104-123159290 bp(+) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

C to A at 123144525 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000035823 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047923]

AlphaFold

Q6NXL1

Predicted Effect

probably benign
Transcript: ENSMUST00000047923

SMART Domains

Protein: ENSMUSP00000035823
Gene: ENSMUSG00000039234

Domain	Start	End	E-Value	Type
low complexity region	46	71	N/A	INTRINSIC
low complexity region	75	87	N/A	INTRINSIC
low complexity region	136	160	N/A	INTRINSIC
low complexity region	197	222	N/A	INTRINSIC
low complexity region	238	256	N/A	INTRINSIC
Pfam:zf-Sec23_Sec24	360	398	1.8e-16	PFAM
Pfam:Sec23_trunk	437	681	3.6e-88	PFAM
Pfam:Sec23_BS	686	770	2e-20	PFAM
Pfam:Sec23_helical	783	884	1e-27	PFAM
Pfam:Gelsolin	899	974	4.2e-12	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000196631

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000197291

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000200309

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.4%
20x: 94.8%

Validation Efficiency

98% (109/111)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the SEC24 subfamily of the SEC23/SEC24 family, which is involved in vesicle trafficking. The encoded protein has similarity to yeast Sec24p component of COPII. COPII is the coat protein complex responsible for vesicle budding from the ER. This gene product is implicated in the shaping of the vesicle, and also in cargo selection and concentration. Mutations in this gene have been associated with Cole-Carpenter syndrome, a disorder affecting bone formation, resulting in craniofacial malformations and bones that break easily. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit early embryonic lethality. A hypomorphic gene trap allele results in lethality during organogenesis. [provided by MGI curators]

Allele List at MGI

All alleles(5) : Gene trapped(5)

Other mutations in this stock

Total: 98 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930579F01Rik	T	C	3: 137,882,346 (GRCm39)	K118R	possibly damaging	Het
Adtrp	T	C	13: 41,920,941 (GRCm39)	T88A	probably damaging	Het
Afap1l1	A	G	18: 61,889,976 (GRCm39)	S87P	probably benign	Het
Ankrd27	A	G	7: 35,303,125 (GRCm39)	K196R	probably benign	Het
Apoe	G	A	7: 19,431,005 (GRCm39)	T79M	probably damaging	Het
Arrdc3	T	A	13: 81,032,011 (GRCm39)	Y81*	probably null	Het
Arrdc3	T	A	13: 81,039,194 (GRCm39)	I75N	probably damaging	Het
Asah2	T	A	19: 31,981,131 (GRCm39)	K629*	probably null	Het
Ass1	A	T	2: 31,404,831 (GRCm39)	N371Y	probably damaging	Het
C130074G19Rik	A	G	1: 184,615,119 (GRCm39)	S24P	probably benign	Het
C87436	A	G	6: 86,423,265 (GRCm39)		probably benign	Het
Calcrl	T	C	2: 84,203,618 (GRCm39)	D54G	probably benign	Het
Clcn2	T	C	16: 20,529,140 (GRCm39)	N367S	probably null	Het
Cnot1	G	T	8: 96,487,969 (GRCm39)	D562E	probably damaging	Het
Commd6	G	A	14: 101,877,709 (GRCm39)		probably benign	Het
Cox6a2	G	A	7: 127,805,212 (GRCm39)		probably benign	Het
Cp	T	A	3: 20,022,287 (GRCm39)	Y230N	probably damaging	Het
Dclre1c	T	C	2: 3,439,032 (GRCm39)	V64A	probably damaging	Het
Eng	T	C	2: 32,567,692 (GRCm39)	V110A	probably damaging	Het
Esyt3	T	C	9: 99,220,860 (GRCm39)	I114M	possibly damaging	Het
Fam83h	A	T	15: 75,875,811 (GRCm39)	Y509N	probably damaging	Het
Fat2	A	T	11: 55,202,075 (GRCm39)	L333H	probably damaging	Het
Fbxo21	A	G	5: 118,146,078 (GRCm39)	N567S	possibly damaging	Het
Fcsk	T	C	8: 111,610,865 (GRCm39)		probably benign	Het
Fn1	A	T	1: 71,634,879 (GRCm39)	L1964Q	probably damaging	Het
Gorasp1	G	T	9: 119,757,312 (GRCm39)	S353R	possibly damaging	Het
Grk2	C	T	19: 4,337,262 (GRCm39)	E646K	probably damaging	Het
Hoxc11	T	C	15: 102,863,397 (GRCm39)	V146A	probably damaging	Het
Igf2bp2	T	C	16: 21,894,841 (GRCm39)	T301A	probably benign	Het
Il11	T	C	7: 4,776,658 (GRCm39)	S111G	probably benign	Het
Ist1	A	T	8: 110,403,418 (GRCm39)	I273K	probably benign	Het
Kdm2b	G	A	5: 123,019,806 (GRCm39)	S738L	probably benign	Het
Lrp2	T	A	2: 69,346,895 (GRCm39)	N784Y	probably benign	Het
Lrp6	T	C	6: 134,462,716 (GRCm39)	E648G	probably damaging	Het
Mapk15	G	A	15: 75,870,103 (GRCm39)	E408K	probably benign	Het
Mdn1	T	A	4: 32,718,317 (GRCm39)	F2191I	possibly damaging	Het
Metrn	C	A	17: 26,015,479 (GRCm39)	V79F	possibly damaging	Het
Mtbp	T	A	15: 55,449,889 (GRCm39)		probably benign	Het
Myh11	C	A	16: 14,041,883 (GRCm39)	Q720H	probably damaging	Het
Myo3a	T	A	2: 22,469,753 (GRCm39)	I508N	probably damaging	Het
Nat9	A	T	11: 115,075,941 (GRCm39)	Y27N	probably damaging	Het
Ncapg2	T	C	12: 116,393,455 (GRCm39)	F553S	probably damaging	Het
Nipsnap3b	T	A	4: 53,015,112 (GRCm39)	L53Q	probably damaging	Het
Nlrp3	A	T	11: 59,449,274 (GRCm39)	H852L	probably benign	Het
Or2d3b	A	G	7: 106,514,226 (GRCm39)	I274V	probably benign	Het
Or2t6	T	A	14: 14,176,092 (GRCm38)		probably benign	Het
Or4a78	T	A	2: 89,497,428 (GRCm39)	K267N	probably damaging	Het
Or52e3	A	T	7: 102,869,558 (GRCm39)	D211V	probably damaging	Het
Or52e3	G	A	7: 102,869,584 (GRCm39)	A220T	probably benign	Het
Or5b122	A	G	19: 13,563,240 (GRCm39)	I191V	probably benign	Het
Pax9	A	G	12: 56,756,528 (GRCm39)	T289A	probably benign	Het
Pcyt2	A	T	11: 120,506,695 (GRCm39)	I53N	possibly damaging	Het
Pdlim4	C	T	11: 53,945,875 (GRCm39)	V327M	probably damaging	Het
Pdzph1	T	A	17: 59,229,756 (GRCm39)		probably benign	Het
Plekhm2	C	T	4: 141,369,704 (GRCm39)		probably benign	Het
Ppt1	T	C	4: 122,742,216 (GRCm39)		probably benign	Het
Prdm1	C	T	10: 44,317,675 (GRCm39)	E398K	probably damaging	Het
Prep	T	C	10: 44,991,174 (GRCm39)	V280A	probably benign	Het
Prkdc	T	A	16: 15,526,565 (GRCm39)		probably benign	Het
Proser3	G	A	7: 30,239,563 (GRCm39)	R514C	probably damaging	Het
Ptk7	G	A	17: 46,883,688 (GRCm39)		probably benign	Het
Rbm45	T	C	2: 76,208,742 (GRCm39)	Y293H	probably damaging	Het
Rnf213	A	C	11: 119,355,878 (GRCm39)	E4108A	possibly damaging	Het
Sdk2	A	G	11: 113,747,581 (GRCm39)	L643P	probably damaging	Het
Sh2d3c	C	G	2: 32,643,033 (GRCm39)	H587D	probably damaging	Het
Slc1a1	G	A	19: 28,878,884 (GRCm39)	G208S	probably benign	Het
Slc35b4	A	T	6: 34,135,452 (GRCm39)	Y287N	probably damaging	Het
Slc46a2	T	A	4: 59,914,544 (GRCm39)	L126F	probably damaging	Het
Slc4a8	T	C	15: 100,698,374 (GRCm39)	M621T	possibly damaging	Het
Slc9b2	T	A	3: 135,042,269 (GRCm39)	V516D	possibly damaging	Het
Slco1a6	T	A	6: 142,102,948 (GRCm39)		probably benign	Het
Sncg	C	T	14: 34,096,495 (GRCm39)	V15I	probably benign	Het
Srgap2	T	C	1: 131,283,302 (GRCm39)	T260A	probably damaging	Het
Stk10	T	A	11: 32,537,305 (GRCm39)		probably benign	Het
Taf5	A	G	19: 47,064,301 (GRCm39)	S415G	possibly damaging	Het
Tdp1	C	T	12: 99,921,217 (GRCm39)		probably benign	Het
Tdp2	T	G	13: 25,025,333 (GRCm39)		probably null	Het
Tgfbi	T	A	13: 56,777,587 (GRCm39)	I357N	probably benign	Het
Tmem116	A	G	5: 121,633,159 (GRCm39)	T178A	probably damaging	Het
Tnrc6a	G	A	7: 122,769,617 (GRCm39)	R469H	probably benign	Het
Top2a	A	T	11: 98,893,729 (GRCm39)	L1055*	probably null	Het
Tox	T	A	4: 6,842,411 (GRCm39)	M40L	probably benign	Het
Trib2	A	T	12: 15,859,930 (GRCm39)	H110Q	probably benign	Het
Trpa1	A	G	1: 14,973,439 (GRCm39)	I293T	possibly damaging	Het
Trpv2	A	G	11: 62,481,086 (GRCm39)	Y395C	probably damaging	Het
Ubn2	T	A	6: 38,411,535 (GRCm39)		probably null	Het
Ubr4	C	T	4: 139,157,487 (GRCm39)	T2348M	probably damaging	Het
Ubxn4	G	A	1: 128,190,641 (GRCm39)	E256K	probably benign	Het
Vmn1r33	C	A	6: 66,589,510 (GRCm39)	G15*	probably null	Het
Vmn1r37	T	A	6: 66,708,769 (GRCm39)	S95T	probably benign	Het
Vmn2r57	A	G	7: 41,050,076 (GRCm39)	C558R	probably damaging	Het
Vnn1	T	C	10: 23,774,500 (GRCm39)		probably null	Het
Vps13c	T	C	9: 67,826,544 (GRCm39)	V1395A	probably benign	Het
Vwa7	A	G	17: 35,238,781 (GRCm39)	I290V	probably benign	Het
Wdr93	A	G	7: 79,408,221 (GRCm39)	E234G	probably damaging	Het
Zfp385b	A	T	2: 77,246,291 (GRCm39)	S245R	probably benign	Het
Zfp942	A	T	17: 22,147,319 (GRCm39)	C437S	probably damaging	Het
Zfyve9	T	A	4: 108,575,902 (GRCm39)	E393V	possibly damaging	Het

Other mutations in Sec24d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01420:Sec24d	APN	3	123,143,658 (GRCm39)	missense	probably benign	0.00
IGL01621:Sec24d	APN	3	123,087,807 (GRCm39)	critical splice acceptor site	probably null
IGL01866:Sec24d	APN	3	123,087,244 (GRCm39)	nonsense	probably null
IGL02064:Sec24d	APN	3	123,137,463 (GRCm39)	splice site	probably benign
IGL02125:Sec24d	APN	3	123,152,607 (GRCm39)	missense	probably damaging	1.00
IGL02173:Sec24d	APN	3	123,147,330 (GRCm39)	missense	probably damaging	1.00
IGL03239:Sec24d	APN	3	123,130,138 (GRCm39)	missense	probably benign	0.00
Scanty	UTSW	3	123,148,596 (GRCm39)	missense	probably damaging	1.00
3-1:Sec24d	UTSW	3	123,147,279 (GRCm39)	missense	possibly damaging	0.94
PIT4531001:Sec24d	UTSW	3	123,136,827 (GRCm39)	missense	probably damaging	1.00
R0838:Sec24d	UTSW	3	123,099,485 (GRCm39)	missense	probably benign	0.08
R1775:Sec24d	UTSW	3	123,130,166 (GRCm39)	missense	probably damaging	1.00
R1895:Sec24d	UTSW	3	123,147,043 (GRCm39)	missense	probably benign	0.04
R1946:Sec24d	UTSW	3	123,147,043 (GRCm39)	missense	probably benign	0.04
R2238:Sec24d	UTSW	3	123,143,543 (GRCm39)	splice site	probably null
R2504:Sec24d	UTSW	3	123,147,255 (GRCm39)	missense	possibly damaging	0.69
R2846:Sec24d	UTSW	3	123,144,395 (GRCm39)	missense	probably damaging	0.98
R2895:Sec24d	UTSW	3	123,136,800 (GRCm39)	missense	probably damaging	1.00
R3428:Sec24d	UTSW	3	123,137,572 (GRCm39)	splice site	probably benign
R4573:Sec24d	UTSW	3	123,152,519 (GRCm39)	missense	probably damaging	1.00
R4668:Sec24d	UTSW	3	123,149,423 (GRCm39)	missense	probably damaging	0.98
R4706:Sec24d	UTSW	3	123,149,427 (GRCm39)	missense	possibly damaging	0.80
R4896:Sec24d	UTSW	3	123,148,596 (GRCm39)	missense	probably damaging	1.00
R4982:Sec24d	UTSW	3	123,093,255 (GRCm39)	missense	probably benign	0.29
R5030:Sec24d	UTSW	3	123,152,550 (GRCm39)	missense	probably damaging	0.98
R5041:Sec24d	UTSW	3	123,087,880 (GRCm39)	missense	probably damaging	0.96
R5078:Sec24d	UTSW	3	123,084,201 (GRCm39)	missense	probably benign	0.00
R5108:Sec24d	UTSW	3	123,099,434 (GRCm39)	splice site	probably null
R5174:Sec24d	UTSW	3	123,158,575 (GRCm39)	missense	probably damaging	0.99
R5661:Sec24d	UTSW	3	123,136,791 (GRCm39)	missense	possibly damaging	0.95
R5661:Sec24d	UTSW	3	123,136,734 (GRCm39)	missense	probably damaging	1.00
R5775:Sec24d	UTSW	3	123,084,109 (GRCm39)	missense	probably benign	0.00
R5859:Sec24d	UTSW	3	123,072,961 (GRCm39)	unclassified	probably benign
R5944:Sec24d	UTSW	3	123,087,230 (GRCm39)	missense	probably benign	0.01
R6053:Sec24d	UTSW	3	123,072,871 (GRCm39)	nonsense	probably null
R6515:Sec24d	UTSW	3	123,136,719 (GRCm39)	missense	possibly damaging	0.92
R6552:Sec24d	UTSW	3	123,084,201 (GRCm39)	missense	probably benign	0.00
R6557:Sec24d	UTSW	3	123,136,736 (GRCm39)	missense	probably damaging	1.00
R6593:Sec24d	UTSW	3	123,147,061 (GRCm39)	missense	probably damaging	1.00
R6594:Sec24d	UTSW	3	123,087,412 (GRCm39)	missense	probably damaging	1.00
R6842:Sec24d	UTSW	3	123,136,868 (GRCm39)	missense	probably benign	0.00
R7072:Sec24d	UTSW	3	123,124,000 (GRCm39)	missense	probably damaging	1.00
R7481:Sec24d	UTSW	3	123,144,412 (GRCm39)	missense	probably damaging	1.00
R7554:Sec24d	UTSW	3	123,149,423 (GRCm39)	missense	probably damaging	1.00
R8270:Sec24d	UTSW	3	123,099,535 (GRCm39)	missense	possibly damaging	0.90
R8481:Sec24d	UTSW	3	123,147,073 (GRCm39)	missense	probably damaging	1.00
R8713:Sec24d	UTSW	3	123,137,541 (GRCm39)	missense	probably damaging	1.00
R8872:Sec24d	UTSW	3	123,148,585 (GRCm39)	splice site	probably benign
R8922:Sec24d	UTSW	3	123,144,488 (GRCm39)	missense	probably damaging	1.00
R8974:Sec24d	UTSW	3	123,099,498 (GRCm39)	missense	probably damaging	1.00
R9015:Sec24d	UTSW	3	123,121,287 (GRCm39)	missense	probably benign	0.43
R9050:Sec24d	UTSW	3	123,144,374 (GRCm39)	missense	probably benign	0.00
R9065:Sec24d	UTSW	3	123,149,452 (GRCm39)	missense	probably damaging	1.00
R9128:Sec24d	UTSW	3	123,087,810 (GRCm39)	missense	probably benign
R9447:Sec24d	UTSW	3	123,084,162 (GRCm39)	missense	probably benign	0.00
R9701:Sec24d	UTSW	3	123,063,321 (GRCm39)	missense	probably damaging	1.00
R9758:Sec24d	UTSW	3	123,136,803 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TTCTGACTGAATGCACACACCTCTG -3'
(R):5'- TGCCTTGCCCATCTGAAGCAAC -3'

Sequencing Primer
(F):5'- GGCTACTGGAGTATCAAATAACCTG -3'
(R):5'- AGCAACACATGTGTGCACAC -3'

Posted On

2013-07-11