Mutagenetix > Incidental Mutation

Incidental Mutation 'R2504:Sec24d'

252097

Institutional Source

Beutler Lab

Gene Symbol

Sec24d

Ensembl Gene

ENSMUSG00000039234

Gene Name

SEC24 homolog D, COPII coat complex component

Synonyms

LOC383951, 2310020L09Rik

MMRRC Submission

040412-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2504 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

123061104-123159290 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 123147255 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 708 (I708T)

Ref Sequence

ENSEMBL: ENSMUSP00000035823 (fasta)

Gene Model

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

AlphaFold

Q6NXL1

Predicted Effect

possibly damaging
Transcript: ENSMUST00000047923
AA Change: I708T

PolyPhen 2 Score 0.695 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000035823
Gene: ENSMUSG00000039234
AA Change: I708T

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

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.4%
20x: 95.4%

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 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: 113 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aatk	T	C	11: 119,909,681 (GRCm39)	D28G	probably benign	Het
Abcg1	T	A	17: 31,311,369 (GRCm39)	S125T	probably damaging	Het
Actbl2	T	C	13: 111,392,717 (GRCm39)	S351P	possibly damaging	Het
Ankrd34b	A	G	13: 92,575,569 (GRCm39)		probably null	Het
BC051665	C	T	13: 60,930,468 (GRCm39)	V295I	probably benign	Het
C1qtnf2	A	G	11: 43,381,983 (GRCm39)	N265S	probably damaging	Het
Ccdc14	C	T	16: 34,542,220 (GRCm39)	R573*	probably null	Het
Cd55b	A	T	1: 130,337,612 (GRCm39)	Y247N	probably damaging	Het
Celsr2	A	T	3: 108,320,907 (GRCm39)	V635E	probably benign	Het
Clec16a	T	C	16: 10,377,551 (GRCm39)		probably benign	Het
Clec4b1	A	G	6: 123,042,904 (GRCm39)	Y41C	probably damaging	Het
Cntn5	A	T	9: 10,172,126 (GRCm39)	D19E	probably benign	Het
Cop1	A	G	1: 159,060,375 (GRCm39)	N53S	probably damaging	Het
Cplane1	G	A	15: 8,248,700 (GRCm39)	E1750K	probably damaging	Het
Csad	A	T	15: 102,097,102 (GRCm39)	M1K	probably null	Het
Cyb5rl	A	G	4: 106,938,142 (GRCm39)	I200V	probably benign	Het
Cyp26a1	A	G	19: 37,686,790 (GRCm39)	T81A	probably damaging	Het
Cyp2d12	A	T	15: 82,443,237 (GRCm39)	H433L	probably benign	Het
D7Ertd443e	T	A	7: 133,951,208 (GRCm39)		probably null	Het
Dennd1b	A	G	1: 139,097,908 (GRCm39)		probably benign	Het
Dmap1	G	T	4: 117,532,495 (GRCm39)	T357K	probably damaging	Het
Dzip1	G	T	14: 119,118,456 (GRCm39)	T759K	probably benign	Het
Elmo2	A	G	2: 165,140,607 (GRCm39)	V300A	probably damaging	Het
Eml5	T	C	12: 98,810,364 (GRCm39)	D864G	possibly damaging	Het
Ep400	A	G	5: 110,816,511 (GRCm39)	V2670A	probably damaging	Het
Epha3	T	A	16: 63,423,988 (GRCm39)	I534F	probably damaging	Het
Epha4	A	C	1: 77,359,628 (GRCm39)	Y742D	probably damaging	Het
Ergic2	A	G	6: 148,106,272 (GRCm39)		probably null	Het
Ero1a	A	T	14: 45,536,545 (GRCm39)		probably null	Het
Fam229a	A	G	4: 129,385,279 (GRCm39)	D70G	probably damaging	Het
Fbn2	C	T	18: 58,226,431 (GRCm39)	R781Q	probably damaging	Het
Fbxo16	A	T	14: 65,508,163 (GRCm39)		probably benign	Het
Fbxo39	T	A	11: 72,208,111 (GRCm39)	S154R	probably benign	Het
Fer	T	A	17: 64,298,575 (GRCm39)		probably null	Het
Filip1l	A	T	16: 57,391,410 (GRCm39)	D428V	probably damaging	Het
Filip1l	A	G	16: 57,391,025 (GRCm39)	I538V	possibly damaging	Het
Fsip2	T	C	2: 82,809,954 (GRCm39)	I2091T	possibly damaging	Het
Glyat	A	C	19: 12,628,762 (GRCm39)	T186P	possibly damaging	Het
Gm10604	A	G	4: 11,980,083 (GRCm39)	S74P	unknown	Het
Gm4787	T	G	12: 81,425,911 (GRCm39)	K82N	possibly damaging	Het
Hectd4	T	C	5: 121,358,683 (GRCm39)	I50T	unknown	Het
Hectd4	T	C	5: 121,402,030 (GRCm39)	S373P	possibly damaging	Het
Hmcn1	A	T	1: 150,562,618 (GRCm39)	C2313*	probably null	Het
Hrob	T	C	11: 102,146,122 (GRCm39)	Y133H	possibly damaging	Het
Igfn1	A	T	1: 135,897,054 (GRCm39)	S1171T	probably benign	Het
Ints8	T	C	4: 11,241,642 (GRCm39)	D267G	probably benign	Het
Itln1	A	G	1: 171,356,727 (GRCm39)	C251R	probably damaging	Het
Jcad	C	T	18: 4,674,026 (GRCm39)	T596M	probably damaging	Het
Kcnj16	C	T	11: 110,916,409 (GRCm39)	T357M	probably benign	Het
Kif13a	G	A	13: 46,967,676 (GRCm39)	T346M	probably damaging	Het
Klhl24	G	A	16: 19,938,917 (GRCm39)	A491T	probably benign	Het
Kntc1	C	T	5: 123,916,410 (GRCm39)	Q748*	probably null	Het
Krt25	T	A	11: 99,208,122 (GRCm39)	K369*	probably null	Het
Krt75	C	T	15: 101,476,466 (GRCm39)	R433Q	probably benign	Het
Krt76	A	G	15: 101,793,293 (GRCm39)	F582L	unknown	Het
Lysmd1	G	A	3: 95,045,708 (GRCm39)	V182I	probably benign	Het
Mab21l2	T	A	3: 86,454,862 (GRCm39)	E46V	probably damaging	Het
Magi2	A	T	5: 20,563,934 (GRCm39)	K355N	probably damaging	Het
Marchf10	T	C	11: 105,276,398 (GRCm39)	D630G	probably damaging	Het
Mast4	A	T	13: 102,875,147 (GRCm39)	I1215N	probably damaging	Het
Nckap1	G	A	2: 80,360,562 (GRCm39)	T523I	probably benign	Het
Nexmif	T	A	X: 103,127,999 (GRCm39)	D1306V	probably damaging	Het
Nfkb1	A	C	3: 135,295,090 (GRCm39)	I918R	possibly damaging	Het
Nt5el	A	G	13: 105,246,250 (GRCm39)	I270M	probably benign	Het
Nup50	A	T	15: 84,817,859 (GRCm39)	T93S	probably benign	Het
Nwd2	T	C	5: 63,961,717 (GRCm39)	Y434H	probably benign	Het
Or13a28	T	C	7: 140,218,397 (GRCm39)	V261A	probably benign	Het
Osbpl1a	C	A	18: 13,038,088 (GRCm39)	V288L	probably benign	Het
Pan3	A	G	5: 147,463,846 (GRCm39)	E562G	possibly damaging	Het
Pappa	T	A	4: 65,099,126 (GRCm39)	Y548*	probably null	Het
Phf3	A	T	1: 30,849,870 (GRCm39)	L1181Q	probably damaging	Het
Phip	T	C	9: 82,797,392 (GRCm39)	H537R	possibly damaging	Het
Pkhd1l1	T	C	15: 44,348,824 (GRCm39)	I240T	probably damaging	Het
Pole	G	A	5: 110,438,368 (GRCm39)		probably null	Het
Polq	T	A	16: 36,832,304 (GRCm39)	S15T	unknown	Het
Prrt2	T	C	7: 126,619,396 (GRCm39)	E23G	possibly damaging	Het
Prss37	A	T	6: 40,494,760 (GRCm39)		probably null	Het
Prune2	T	C	19: 16,977,400 (GRCm39)	L45P	probably damaging	Het
Psd	A	T	19: 46,313,352 (GRCm39)	M6K	possibly damaging	Het
Psmd1	A	G	1: 86,017,719 (GRCm39)	E510G	possibly damaging	Het
Ptch1	T	G	13: 63,672,773 (GRCm39)	E944A	probably benign	Het
Pxdn	T	A	12: 30,053,405 (GRCm39)	I1194N	probably damaging	Het
Rbp3	C	T	14: 33,677,975 (GRCm39)	T641M	probably damaging	Het
Rgmb	C	A	17: 16,027,909 (GRCm39)	R270L	probably benign	Het
Rpgrip1l	A	G	8: 92,007,344 (GRCm39)		probably null	Het
Rps2	G	A	17: 24,939,353 (GRCm39)		probably benign	Het
Rsbn1l	G	T	5: 21,107,364 (GRCm39)	A550E	probably damaging	Het
S1pr4	C	T	10: 81,335,138 (GRCm39)	R112H	probably benign	Het
Scfd2	T	C	5: 74,691,838 (GRCm39)	N148S	probably damaging	Het
Scin	C	T	12: 40,131,705 (GRCm39)	M276I	probably benign	Het
Skint11	T	A	4: 114,086,009 (GRCm39)	F41I	possibly damaging	Het
Slc15a4	A	T	5: 127,694,303 (GRCm39)	F44Y	possibly damaging	Het
Slc6a18	A	G	13: 73,823,925 (GRCm39)	Y72H	probably benign	Het
Slc7a11	A	T	3: 50,332,195 (GRCm39)		probably null	Het
Slc7a14	G	T	3: 31,291,650 (GRCm39)	N209K	possibly damaging	Het
Sstr2	T	C	11: 113,515,257 (GRCm39)	C59R	probably damaging	Het
Stab1	A	G	14: 30,884,997 (GRCm39)		probably null	Het
Stag1	G	T	9: 100,748,263 (GRCm39)	S475I	probably damaging	Het
Stxbp5l	A	G	16: 36,936,029 (GRCm39)	Y1183H	probably damaging	Het
Svep1	A	T	4: 58,135,628 (GRCm39)		probably null	Het
Tm9sf2	A	G	14: 122,396,096 (GRCm39)	T653A	probably benign	Het
Tmeff1	T	C	4: 48,662,059 (GRCm39)	S366P	possibly damaging	Het
Tnnt2	G	T	1: 135,779,803 (GRCm39)	W300L	probably damaging	Het
Traj32	A	G	14: 54,423,560 (GRCm39)		probably benign	Het
Trp53bp2	A	T	1: 182,269,204 (GRCm39)	M223L	probably benign	Het
Tsga10	G	A	1: 37,854,758 (GRCm39)	T246M	probably damaging	Het
Txn2	A	T	15: 77,810,870 (GRCm39)		probably benign	Het
Ubr3	T	A	2: 69,768,542 (GRCm39)	F450I	probably damaging	Het
Usp47	T	C	7: 111,703,677 (GRCm39)		probably null	Het
Vars2	C	T	17: 35,975,685 (GRCm39)	R244Q	probably damaging	Het
Xrra1	T	A	7: 99,546,803 (GRCm39)	F251L	probably damaging	Het
Zfp804a	G	A	2: 82,087,863 (GRCm39)	R564Q	probably benign	Het
Zfp983	T	C	17: 21,877,883 (GRCm39)	C29R	probably 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
R0008:Sec24d	UTSW	3	123,144,525 (GRCm39)	splice site	probably benign
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
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'- ACATTCAGATAGCCAAAGGTTTCTG -3'
(R):5'- ACTCTAAGGACTCCTGCTTGG -3'

Sequencing Primer
(F):5'- CGACCTCCGGAATGATATTGAG -3'
(R):5'- CCTGCTTGGGAGAAAGAGTTC -3'

Posted On

2014-12-04