Mutagenetix > Incidental Mutation

Incidental Mutation 'R1895:Sec24d'

209718

Institutional Source

Beutler Lab

Gene Symbol

Sec24d

Ensembl Gene

ENSMUSG00000039234

Gene Name

SEC24 homolog D, COPII coat complex component

Synonyms

LOC383951, 2310020L09Rik

MMRRC Submission

039915-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1895 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

123061104-123159290 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 123147043 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Leucine at position 667 (H667L)

Ref Sequence

ENSEMBL: ENSMUSP00000035823 (fasta)

Gene Model

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

AlphaFold

Q6NXL1

Predicted Effect

probably benign
Transcript: ENSMUST00000047923
AA Change: H667L

PolyPhen 2 Score 0.043 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000035823
Gene: ENSMUSG00000039234
AA Change: H667L

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

0.1381

Coding Region Coverage

1x: 97.1%
3x: 96.2%
10x: 93.2%
20x: 86.6%

Validation Efficiency

96% (100/104)

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aasdh	A	G	5: 77,039,551 (GRCm39)	S253P	probably damaging	Het
Adgrb1	A	G	15: 74,412,314 (GRCm39)	D431G	probably damaging	Het
Adgrv1	C	T	13: 81,522,368 (GRCm39)	C5923Y	probably damaging	Het
Akr1b10	T	A	6: 34,365,805 (GRCm39)	I110N	probably damaging	Het
Apba2	T	C	7: 64,394,378 (GRCm39)		probably null	Het
Arhgef12	G	T	9: 42,917,152 (GRCm39)	Q396K	probably damaging	Het
Arpc1b	A	G	5: 145,059,443 (GRCm39)	T56A	probably null	Het
Atoh1	T	C	6: 64,706,443 (GRCm39)	V46A	probably benign	Het
AU015836	T	C	X: 93,012,985 (GRCm39)		probably benign	Het
Cacna1c	C	T	6: 118,589,586 (GRCm39)	R1446H	probably damaging	Het
Capn13	T	C	17: 73,657,520 (GRCm39)	E240G	possibly damaging	Het
Cdh8	T	C	8: 100,006,189 (GRCm39)	T133A	possibly damaging	Het
Cep295	T	C	9: 15,243,399 (GRCm39)	T1686A	possibly damaging	Het
Col4a3	A	T	1: 82,656,829 (GRCm39)	K749N	unknown	Het
Col6a3	T	A	1: 90,731,433 (GRCm39)	M1000L	probably benign	Het
Coq8b	G	A	7: 26,939,299 (GRCm39)	V150I	possibly damaging	Het
Dmxl1	G	T	18: 50,088,981 (GRCm39)		probably null	Het
Dnah10	A	G	5: 124,835,494 (GRCm39)	D990G	probably benign	Het
Dpp7	G	T	2: 25,243,691 (GRCm39)		probably null	Het
Eif3l	A	G	15: 78,973,677 (GRCm39)	N364S	possibly damaging	Het
Epb41l5	T	C	1: 119,476,902 (GRCm39)	D718G	possibly damaging	Het
F930017D23Rik	G	A	10: 43,469,440 (GRCm39)		noncoding transcript	Het
Fam20a	T	C	11: 109,564,380 (GRCm39)	K458E	probably benign	Het
Fbxo44	C	G	4: 148,240,726 (GRCm39)	R220S	probably damaging	Het
Fut2	A	G	7: 45,300,748 (GRCm39)	F8S	probably damaging	Het
Gad2	A	T	2: 22,575,440 (GRCm39)	T515S	probably benign	Het
Glmn	T	C	5: 107,718,110 (GRCm39)	D269G	probably benign	Het
Gpatch4	A	G	3: 87,959,409 (GRCm39)	Y106C	probably damaging	Het
Grm3	A	G	5: 9,562,123 (GRCm39)	W576R	probably damaging	Het
Hdac7	T	C	15: 97,694,767 (GRCm39)	D701G	probably damaging	Het
Hectd2	T	A	19: 36,591,860 (GRCm39)	I687K	probably damaging	Het
Hmcn2	T	C	2: 31,295,647 (GRCm39)	S2619P	probably damaging	Het
Ilf3	T	A	9: 21,316,063 (GRCm39)		probably benign	Het
Kdm4b	T	A	17: 56,704,340 (GRCm39)	V272E	probably damaging	Het
Kera	A	G	10: 97,445,009 (GRCm39)	K123E	probably benign	Het
Kif11	G	A	19: 37,375,847 (GRCm39)	R220K	probably damaging	Het
Kmt2c	A	T	5: 25,520,152 (GRCm39)	V1986E	probably benign	Het
Lrp11	T	C	10: 7,499,540 (GRCm39)	Y244H	probably damaging	Het
Lrp1b	T	A	2: 40,555,159 (GRCm39)	D320V	unknown	Het
Map4k5	A	T	12: 69,892,529 (GRCm39)	D133E	probably damaging	Het
Megf11	A	T	9: 64,586,558 (GRCm39)	D461V	probably damaging	Het
Muc5b	A	C	7: 141,411,382 (GRCm39)	T1443P	unknown	Het
Mxi1	G	A	19: 53,358,775 (GRCm39)	R236H	probably benign	Het
Nav1	A	T	1: 135,386,396 (GRCm39)	W1211R	probably damaging	Het
Ncoa3	T	A	2: 165,901,097 (GRCm39)	N896K	possibly damaging	Het
Nmt2	T	A	2: 3,323,672 (GRCm39)	I355N	probably benign	Het
Nxpe5	T	C	5: 138,249,785 (GRCm39)	V525A	probably damaging	Het
Oas1f	A	T	5: 120,993,648 (GRCm39)	T287S	probably benign	Het
Or1n1b	A	T	2: 36,780,458 (GRCm39)	M134K	possibly damaging	Het
Or5ae1	T	C	7: 84,565,487 (GRCm39)	S167P	probably benign	Het
Or6ae1	T	A	7: 139,742,726 (GRCm39)	I46F	possibly damaging	Het
Or7a38	T	A	10: 78,752,758 (GRCm39)	I28N	probably damaging	Het
Or8b3	T	A	9: 38,314,182 (GRCm39)	M1K	probably null	Het
Pakap	T	C	4: 57,638,068 (GRCm39)	V35A	probably benign	Het
Panx1	A	G	9: 14,918,822 (GRCm39)	C346R	probably benign	Het
Plekha7	T	C	7: 115,744,209 (GRCm39)	E764G	probably damaging	Het
Plet1	A	G	9: 50,415,652 (GRCm39)		probably null	Het
Plod2	A	G	9: 92,489,188 (GRCm39)	S707G	probably damaging	Het
Plscr4	G	A	9: 92,365,889 (GRCm39)	V120I	probably damaging	Het
Pramel31	T	A	4: 144,088,435 (GRCm39)	V77E	probably benign	Het
Prob1	T	A	18: 35,785,942 (GRCm39)	T771S	possibly damaging	Het
Rasa3	A	G	8: 13,681,768 (GRCm39)		probably benign	Het
Ror2	T	C	13: 53,285,885 (GRCm39)	I110V	probably damaging	Het
Sema3d	A	G	5: 12,623,810 (GRCm39)	Q573R	probably damaging	Het
Serpinb2	T	A	1: 107,452,337 (GRCm39)	V305D	probably damaging	Het
Slc11a2	G	A	15: 100,301,775 (GRCm39)	R249C	probably benign	Het
Slc14a1	T	C	18: 78,152,912 (GRCm39)	I276V	possibly damaging	Het
Snx19	T	A	9: 30,343,620 (GRCm39)	N593K	probably damaging	Het
Ssh2	C	G	11: 77,340,571 (GRCm39)	D574E	probably damaging	Het
Stil	T	C	4: 114,881,072 (GRCm39)	S539P	probably benign	Het
Syt4	T	C	18: 31,577,141 (GRCm39)	K71R	probably damaging	Het
Tenm4	A	T	7: 96,385,015 (GRCm39)	H524L	probably damaging	Het
Tex30	C	T	1: 44,130,564 (GRCm39)	G68D	probably damaging	Het
Tm4sf19	A	G	16: 32,226,500 (GRCm39)	Y138C	probably damaging	Het
Tmem43	A	T	6: 91,463,891 (GRCm39)	I389F	probably benign	Het
Trpm1	A	T	7: 63,873,556 (GRCm39)	N488Y	probably damaging	Het
Tshz1	A	T	18: 84,031,558 (GRCm39)	L950Q	probably damaging	Het
Vmn1r16	T	C	6: 57,299,885 (GRCm39)	I246V	probably benign	Het
Vmn1r188	T	G	13: 22,272,815 (GRCm39)	S256R	possibly damaging	Het
Zfp12	G	A	5: 143,231,133 (GRCm39)	E487K	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
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'- TCTTCCCATCCAAAGGTTATGAAG -3'
(R):5'- GGGACAAAGGAAGATTTGCCTC -3'

Sequencing Primer
(F):5'- AAGAGTCACACTGCCAAAGATTATG -3'
(R):5'- GACAAAGGAAGATTTGCCTCTTCTTC -3'

Posted On

2014-06-30