Mutagenetix > Incidental Mutation

Incidental Mutation 'R5303:Tmed1'

404357

Institutional Source

Beutler Lab

Gene Symbol

Tmed1

Ensembl Gene

ENSMUSG00000032180

Gene Name

transmembrane p24 trafficking protein 1

Synonyms

St2l, Ly84l, Il1rl1l

MMRRC Submission

042886-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.126) question?

Stock #

R5303 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

21418849-21421548 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 21421343 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Lysine at position 44 (Q44K)

Ref Sequence

ENSEMBL: ENSMUSP00000034698 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000034698] [ENSMUST00000072362] [ENSMUST00000091087] [ENSMUST00000115404] [ENSMUST00000165766] [ENSMUST00000172482] [ENSMUST00000214576] [ENSMUST00000214285] [ENSMUST00000173397]

AlphaFold

Q3V009

Predicted Effect

possibly damaging
Transcript: ENSMUST00000034698
AA Change: Q44K

PolyPhen 2 Score 0.518 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000034698
Gene: ENSMUSG00000032180
AA Change: Q44K

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
EMP24_GP25L	33	220	1.78e-54	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000072362

SMART Domains

Protein: ENSMUSP00000072199
Gene: ENSMUSG00000033335

Domain	Start	End	E-Value	Type
DYNc	6	245	1.01e-193	SMART
low complexity region	298	313	N/A	INTRINSIC
PH	520	627	8e-13	SMART
GED	648	739	2.57e-28	SMART
low complexity region	740	752	N/A	INTRINSIC
low complexity region	777	799	N/A	INTRINSIC
low complexity region	831	864	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000091087

SMART Domains

Protein: ENSMUSP00000088616
Gene: ENSMUSG00000033335

Domain	Start	End	E-Value	Type
DYNc	6	245	1.01e-193	SMART
low complexity region	298	313	N/A	INTRINSIC
PH	516	623	8e-13	SMART
GED	644	735	2.57e-28	SMART
low complexity region	736	748	N/A	INTRINSIC
low complexity region	773	795	N/A	INTRINSIC
low complexity region	827	860	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000115404

SMART Domains

Protein: ENSMUSP00000111063
Gene: ENSMUSG00000033335

Domain	Start	End	E-Value	Type
DYNc	6	245	1.01e-193	SMART
low complexity region	298	313	N/A	INTRINSIC
PH	520	627	8e-13	SMART
GED	648	739	2.57e-28	SMART
low complexity region	740	752	N/A	INTRINSIC
low complexity region	777	799	N/A	INTRINSIC
low complexity region	831	864	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000165766

SMART Domains

Protein: ENSMUSP00000128961
Gene: ENSMUSG00000033335

Domain	Start	End	E-Value	Type
DYNc	6	245	1.01e-193	SMART
low complexity region	298	313	N/A	INTRINSIC
PH	520	627	8e-13	SMART
GED	648	739	2.57e-28	SMART
low complexity region	740	752	N/A	INTRINSIC
low complexity region	777	799	N/A	INTRINSIC
low complexity region	831	858	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000172482

SMART Domains

Protein: ENSMUSP00000133564
Gene: ENSMUSG00000033335

Domain	Start	End	E-Value	Type
DYNc	6	245	1.01e-193	SMART
low complexity region	298	313	N/A	INTRINSIC
PH	520	627	8e-13	SMART
GED	648	739	2.57e-28	SMART
low complexity region	740	752	N/A	INTRINSIC
low complexity region	777	799	N/A	INTRINSIC
low complexity region	831	864	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000172763

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174243

Predicted Effect

possibly damaging
Transcript: ENSMUST00000214576
AA Change: Q44K

PolyPhen 2 Score 0.461 (Sensitivity: 0.89; Specificity: 0.90)

Predicted Effect

unknown
Transcript: ENSMUST00000213167
AA Change: Q39K

Predicted Effect

unknown
Transcript: ENSMUST00000214285
AA Change: Q44K

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000213316

Predicted Effect

probably benign
Transcript: ENSMUST00000174050

SMART Domains

Protein: ENSMUSP00000134696
Gene: ENSMUSG00000033335

Domain	Start	End	E-Value	Type
DYNc	1	196	8.6e-138	SMART
low complexity region	249	264	N/A	INTRINSIC
PH	467	574	8e-13	SMART
GED	595	686	2.57e-28	SMART
low complexity region	687	699	N/A	INTRINSIC
low complexity region	724	746	N/A	INTRINSIC
low complexity region	778	805	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000173397

SMART Domains

Protein: ENSMUSP00000134243
Gene: ENSMUSG00000033335

Domain	Start	End	E-Value	Type
DYNc	6	245	1.01e-193	SMART
low complexity region	298	313	N/A	INTRINSIC
PH	520	627	8e-13	SMART
GED	648	739	2.57e-28	SMART
low complexity region	740	752	N/A	INTRINSIC
low complexity region	777	799	N/A	INTRINSIC
low complexity region	831	863	N/A	INTRINSIC

Meta Mutation Damage Score

0.2139

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.6%
20x: 95.9%

Validation Efficiency

98% (63/64)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the TMED (transmembrane emp24 domain-containing) protein family, which is involved in the vesicular trafficking of proteins. The protein encoded by this gene was identified by its interaction with interleukin 1 receptor-like 1 (IL1RL1) and may play a role in innate immunity. This protein lacks any similarity to other interleukin 1 ligands. Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jul 2013]

Allele List at MGI

Other mutations in this stock

Total: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700006A11Rik	C	G	3: 124,199,999 (GRCm39)	G531A	probably damaging	Het
4921504E06Rik	A	G	2: 19,521,110 (GRCm39)	Y256H	possibly damaging	Het
Abcc12	C	A	8: 87,236,415 (GRCm39)	R1133L	probably benign	Het
Acss3	T	A	10: 106,920,712 (GRCm39)	T133S	possibly damaging	Het
Adra1d	G	A	2: 131,388,169 (GRCm39)	P462L	possibly damaging	Het
Ank2	A	T	3: 126,739,453 (GRCm39)		probably benign	Het
Arid2	G	A	15: 96,290,349 (GRCm39)	R1748Q	probably damaging	Het
B3glct	C	T	5: 149,677,488 (GRCm39)		probably benign	Het
C3ar1	A	T	6: 122,826,794 (GRCm39)	S474R	probably damaging	Het
Cd1d1	A	G	3: 86,905,427 (GRCm39)	F189L	probably benign	Het
Cd46	T	C	1: 194,744,707 (GRCm39)	I344V	probably benign	Het
Chrna1	T	C	2: 73,396,618 (GRCm39)	M426V	probably benign	Het
Cinp	G	A	12: 110,843,295 (GRCm39)	T139M	probably damaging	Het
Cplane1	G	A	15: 8,290,174 (GRCm39)		probably null	Het
Disp2	T	C	2: 118,641,329 (GRCm39)		probably benign	Het
Dnaaf6rt	G	A	1: 31,262,537 (GRCm39)	R173H	probably damaging	Het
Eapp	G	A	12: 54,739,703 (GRCm39)	P38L	probably damaging	Het
Eif4g3	T	C	4: 137,853,873 (GRCm39)	S480P	probably benign	Het
Epb41l3	G	C	17: 69,564,444 (GRCm39)	E390Q	probably damaging	Het
Fermt1	T	C	2: 132,753,259 (GRCm39)		probably null	Het
Foxf2	T	A	13: 31,810,463 (GRCm39)	F134Y	possibly damaging	Het
Foxp2	T	A	6: 15,324,636 (GRCm39)	C95S	probably benign	Het
Gm11595	G	A	11: 99,663,381 (GRCm39)	R100C	unknown	Het
Gria1	A	G	11: 57,133,851 (GRCm39)	T577A	probably benign	Het
Hal	A	G	10: 93,352,227 (GRCm39)		probably benign	Het
Hdac7	C	A	15: 97,695,899 (GRCm39)	E670D	probably damaging	Het
Islr2	A	T	9: 58,115,558 (GRCm39)		probably benign	Het
Itpr3	T	C	17: 27,335,663 (GRCm39)	Y2258H	probably benign	Het
Mical3	G	T	6: 120,936,941 (GRCm39)	T1195K	probably benign	Het
Myh1	T	C	11: 67,092,843 (GRCm39)	S46P	probably benign	Het
Mylk3	T	A	8: 86,077,105 (GRCm39)	I444F	probably damaging	Het
Nlrc3	A	T	16: 3,781,478 (GRCm39)	C644S	probably benign	Het
Notch1	C	T	2: 26,368,631 (GRCm39)	V553M	probably benign	Het
Or10g9	A	G	9: 39,911,884 (GRCm39)	I213T	probably damaging	Het
Or4a72	T	A	2: 89,405,345 (GRCm39)	I242F	possibly damaging	Het
Or51a43	T	C	7: 103,718,239 (GRCm39)		probably benign	Het
Or5b102	T	A	19: 13,041,139 (GRCm39)	Y121*	probably null	Het
Postn	A	G	3: 54,285,018 (GRCm39)	T669A	probably damaging	Het
Ppp5c	G	T	7: 16,739,209 (GRCm39)	Q472K	probably benign	Het
Qsox1	T	C	1: 155,655,039 (GRCm39)	H708R	probably benign	Het
Rhbdl2	A	G	4: 123,704,014 (GRCm39)		probably benign	Het
Ryr1	C	T	7: 28,767,907 (GRCm39)	E2884K	probably damaging	Het
Saysd1	T	C	14: 20,133,026 (GRCm39)	T44A	probably benign	Het
Septin14	T	A	5: 129,766,712 (GRCm39)	M290L	possibly damaging	Het
Sh3bp5	C	A	14: 31,099,452 (GRCm39)	R265L	probably benign	Het
Slc38a8	C	A	8: 120,212,780 (GRCm39)	V294L	possibly damaging	Het
Spdye4b	C	T	5: 143,188,158 (GRCm39)	T217I	probably benign	Het
Sugp2	T	A	8: 70,694,827 (GRCm39)		probably benign	Het
Syne1	T	C	10: 5,370,464 (GRCm39)	T232A	probably benign	Het
Tbc1d5	A	T	17: 51,043,228 (GRCm39)	D753E	probably benign	Het
Ttc6	T	A	12: 57,622,606 (GRCm39)	S2T	possibly damaging	Het
Ube4b	T	C	4: 149,468,260 (GRCm39)	D172G	probably damaging	Het
Vmn1r235	C	A	17: 21,482,268 (GRCm39)	Q198K	probably benign	Het
Wdfy3	T	C	5: 102,100,849 (GRCm39)	H256R	probably damaging	Het
Zfat	A	T	15: 67,982,335 (GRCm39)	H1059Q	probably damaging	Het
Zfp758	A	G	17: 22,593,842 (GRCm39)	I77M	probably benign	Het
Zfp850	C	T	7: 27,707,838 (GRCm39)	A2T	probably damaging	Het
Zfyve1	A	T	12: 83,621,830 (GRCm39)	N188K	probably damaging	Het
Zyg11a	C	T	4: 108,041,629 (GRCm39)		probably null	Het

Other mutations in Tmed1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01308:Tmed1	APN	9	21,421,338 (GRCm39)	nonsense	probably null
IGL01343:Tmed1	APN	9	21,421,369 (GRCm39)	missense	probably damaging	1.00
R1866:Tmed1	UTSW	9	21,420,387 (GRCm39)	missense	probably damaging	1.00
R5768:Tmed1	UTSW	9	21,420,619 (GRCm39)	missense	probably benign	0.07
R7117:Tmed1	UTSW	9	21,420,550 (GRCm39)	missense	possibly damaging	0.49

Predicted Primers

PCR Primer
(F):5'- ATGCCCCTTCTCTGCAAGAC -3'
(R):5'- TTTGGGGTCGAACAGAAGCC -3'

Sequencing Primer
(F):5'- AAGACTATTAGCGTTCTGGCCAC -3'
(R):5'- AAGCCAATGAGCTTTGCCG -3'

Posted On

2016-07-22