Mutagenetix > Incidental Mutation

Incidental Mutation 'R5109:Tmem39a'

393769

Institutional Source

Beutler Lab

Gene Symbol

Tmem39a

Ensembl Gene

ENSMUSG00000002845

Gene Name

transmembrane protein 39a

Synonyms

MMRRC Submission

042697-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.197) question?

Stock #

R5109 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

38379060-38412524 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 38411326 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Aspartic acid at position 359 (G359D)

Ref Sequence

ENSEMBL: ENSMUSP00000126218 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000002924] [ENSMUST00000163884] [ENSMUST00000163948] [ENSMUST00000171687]

AlphaFold

Q9CYC3

Predicted Effect

possibly damaging
Transcript: ENSMUST00000002924
AA Change: G427D

PolyPhen 2 Score 0.940 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000002924
Gene: ENSMUSG00000002845
AA Change: G427D

Domain	Start	End	E-Value	Type
Pfam:Tmp39	40	476	9.4e-198	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000163549

Predicted Effect

possibly damaging
Transcript: ENSMUST00000163884
AA Change: G427D

PolyPhen 2 Score 0.940 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000132515
Gene: ENSMUSG00000002845
AA Change: G427D

Domain	Start	End	E-Value	Type
low complexity region	26	41	N/A	INTRINSIC
Pfam:Tmp39	42	475	1.3e-198	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000163948

SMART Domains

Protein: ENSMUSP00000130791
Gene: ENSMUSG00000002845

Domain	Start	End	E-Value	Type
low complexity region	26	34	N/A	INTRINSIC
Pfam:Tmp39	35	164	7.1e-44	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000165140

Predicted Effect

probably benign
Transcript: ENSMUST00000165631

SMART Domains

Protein: ENSMUSP00000130186
Gene: ENSMUSG00000002845

Domain	Start	End	E-Value	Type
Pfam:Tmp39	1	101	9.7e-49	PFAM
Pfam:Tmp39	99	134	1.7e-18	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000166854

SMART Domains

Protein: ENSMUSP00000127040
Gene: ENSMUSG00000002845

Domain	Start	End	E-Value	Type
Pfam:Tmp39	1	152	4.9e-44	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000170097

Predicted Effect

probably damaging
Transcript: ENSMUST00000171687
AA Change: G359D

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000126218
Gene: ENSMUSG00000002845
AA Change: G359D

Domain	Start	End	E-Value	Type
Pfam:Tmp39	40	192	4.4e-62	PFAM
Pfam:Tmp39	193	408	4.2e-119	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000171064

Predicted Effect

probably benign
Transcript: ENSMUST00000169554

SMART Domains

Protein: ENSMUSP00000127143
Gene: ENSMUSG00000002845

Domain	Start	End	E-Value	Type
Pfam:Tmp39	1	190	2.2e-69	PFAM

Meta Mutation Damage Score

0.3351

Coding Region Coverage

1x: 99.1%
3x: 98.2%
10x: 95.9%
20x: 91.2%

Validation Efficiency

95% (78/82)

Allele List at MGI

Other mutations in this stock

Total: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ankrd17	T	C	5: 90,391,395 (GRCm39)	S1841G	possibly damaging	Het
Anxa10	T	C	8: 62,516,093 (GRCm39)	E193G	possibly damaging	Het
Ap3d1	T	C	10: 80,545,284 (GRCm39)	S1056G	probably benign	Het
Apbb1	T	C	7: 105,214,242 (GRCm39)	N62D	probably damaging	Het
Apobec2	A	T	17: 48,730,022 (GRCm39)	Y215N	probably damaging	Het
Apobec2	T	A	17: 48,730,024 (GRCm39)	Y214F	probably damaging	Het
Appl2	A	T	10: 83,436,871 (GRCm39)	V630E	probably benign	Het
Bud23	T	C	5: 135,089,877 (GRCm39)		probably benign	Het
Cacna1b	A	T	2: 24,580,797 (GRCm39)	M683K	possibly damaging	Het
Cbfa2t2	T	A	2: 154,373,293 (GRCm39)	D187E	probably damaging	Het
Cfap54	G	T	10: 92,773,753 (GRCm39)	F96L	probably benign	Het
Cimap1a	A	T	7: 140,429,461 (GRCm39)	S197C	probably benign	Het
Crebbp	A	G	16: 3,906,295 (GRCm39)		probably benign	Het
Crocc	C	T	4: 140,755,722 (GRCm39)	R1102Q	probably damaging	Het
Dcaf12	T	C	4: 41,298,329 (GRCm39)	D273G	possibly damaging	Het
Dchs1	T	C	7: 105,414,221 (GRCm39)	T865A	probably benign	Het
Dhfr	A	T	13: 92,491,788 (GRCm39)	I8F	probably damaging	Het
Dnaja2	A	T	8: 86,279,887 (GRCm39)	F97L	possibly damaging	Het
Dnase1l1	C	T	X: 73,320,644 (GRCm39)		probably null	Het
Doc2b	T	C	11: 75,667,967 (GRCm39)	D261G	probably benign	Het
Ear1	A	G	14: 44,056,485 (GRCm39)	Y128H	probably benign	Het
Elac2	T	A	11: 64,883,142 (GRCm39)	I171N	probably damaging	Het
Entpd3	C	A	9: 120,395,380 (GRCm39)	N454K	possibly damaging	Het
Flrt3	A	G	2: 140,502,663 (GRCm39)	S322P	possibly damaging	Het
Fn1	C	T	1: 71,688,394 (GRCm39)	C170Y	probably damaging	Het
Gabbr1	T	A	17: 37,382,920 (GRCm39)		probably benign	Het
Gm7247	T	G	14: 51,602,774 (GRCm39)	S37A	probably damaging	Het
Gm8775	T	A	3: 4,277,008 (GRCm39)		noncoding transcript	Het
Gprc5c	G	T	11: 114,755,093 (GRCm39)	V257L	possibly damaging	Het
Gria4	A	C	9: 4,472,168 (GRCm39)	N440K	probably damaging	Het
H2-T22	T	A	17: 36,350,113 (GRCm39)	R334*	probably null	Het
Ift172	T	C	5: 31,423,330 (GRCm39)	D817G	probably benign	Het
Igkv9-124	T	A	6: 67,919,348 (GRCm39)	R21S	possibly damaging	Het
Itgam	G	A	7: 127,712,390 (GRCm39)	V846I	probably benign	Het
Kif11	T	A	19: 37,373,063 (GRCm39)	M94K	possibly damaging	Het
Krtcap2	T	C	3: 89,154,085 (GRCm39)	V2A	probably benign	Het
Lrrc47	A	G	4: 154,101,933 (GRCm39)	D400G	probably damaging	Het
Man2a1	T	A	17: 65,059,443 (GRCm39)	V1110E	probably benign	Het
Mfsd9	T	A	1: 40,813,365 (GRCm39)	I317F	probably damaging	Het
Mindy4	A	T	6: 55,193,730 (GRCm39)		probably null	Het
Mrpl53	A	G	6: 83,086,541 (GRCm39)	T82A	probably damaging	Het
Myo3b	A	G	2: 69,925,637 (GRCm39)	K35E	possibly damaging	Het
Nalcn	A	G	14: 123,515,650 (GRCm39)	V1717A	possibly damaging	Het
Ncoa2	A	G	1: 13,257,070 (GRCm39)	V143A	probably damaging	Het
Ndufa9	A	C	6: 126,809,520 (GRCm39)		probably null	Het
Or10ag60	G	A	2: 87,438,319 (GRCm39)	G196R	possibly damaging	Het
Or10ag60	G	A	2: 87,437,755 (GRCm39)	A8T	possibly damaging	Het
Or12e9	A	G	2: 87,201,878 (GRCm39)	M1V	probably null	Het
Or5k17	A	G	16: 58,746,422 (GRCm39)	S171P	probably benign	Het
Or5p55	T	C	7: 107,567,104 (GRCm39)	S167P	probably benign	Het
Or6c202	T	C	10: 128,996,106 (GRCm39)	Y249C	probably damaging	Het
Or7g28	A	T	9: 19,272,438 (GRCm39)	I71N	probably damaging	Het
Or9g8	G	A	2: 85,607,668 (GRCm39)	V247M	probably damaging	Het
Pde4b	G	T	4: 102,458,741 (GRCm39)	A466S	probably damaging	Het
Pfkfb3	A	T	2: 11,491,162 (GRCm39)		probably benign	Het
Ppp1r21	A	G	17: 88,866,268 (GRCm39)	K355E	probably damaging	Het
Psme4	T	A	11: 30,741,095 (GRCm39)	Y90*	probably null	Het
Rbms1	G	A	2: 60,612,284 (GRCm39)	L161F	probably damaging	Het
Rdh16f2	A	G	10: 127,702,672 (GRCm39)	D83G	probably damaging	Het
Sec16b	C	T	1: 157,392,361 (GRCm39)	R910*	probably null	Het
Sema4c	CTGGGCTT	C	1: 36,591,381 (GRCm39)		probably null	Het
Spata31e5	T	C	1: 28,816,636 (GRCm39)	I465M	possibly damaging	Het
Stambp	A	G	6: 83,540,803 (GRCm39)		probably null	Het
Tcf21	T	C	10: 22,695,558 (GRCm39)	N82S	probably damaging	Het
Tlr2	A	T	3: 83,745,030 (GRCm39)	V351D	probably damaging	Het
Ttc23l	G	T	15: 10,551,636 (GRCm39)	T30K	possibly damaging	Het
Vmn2r17	C	A	5: 109,577,342 (GRCm39)	F464L	probably benign	Het
Vmn2r49	T	A	7: 9,710,204 (GRCm39)	T843S	probably benign	Het
Vmn2r7	T	C	3: 64,598,088 (GRCm39)	D823G	probably null	Het
Wrnip1	T	A	13: 33,000,319 (GRCm39)	L442Q	probably damaging	Het
Zbtb38	G	T	9: 96,569,062 (GRCm39)	S674Y	probably damaging	Het
Zfp639	T	G	3: 32,574,585 (GRCm39)		probably null	Het

Other mutations in Tmem39a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL03276:Tmem39a	APN	16	38,405,646 (GRCm39)	missense	probably benign	0.01
R0270:Tmem39a	UTSW	16	38,384,675 (GRCm39)	splice site	probably benign
R0382:Tmem39a	UTSW	16	38,411,760 (GRCm39)	utr 3 prime	probably benign
R0539:Tmem39a	UTSW	16	38,411,337 (GRCm39)	missense	probably benign	0.00
R0743:Tmem39a	UTSW	16	38,405,764 (GRCm39)	missense	probably damaging	1.00
R1324:Tmem39a	UTSW	16	38,393,531 (GRCm39)	missense	possibly damaging	0.84
R4052:Tmem39a	UTSW	16	38,406,650 (GRCm39)	missense	probably damaging	1.00
R4799:Tmem39a	UTSW	16	38,411,524 (GRCm39)	utr 3 prime	probably benign
R4919:Tmem39a	UTSW	16	38,405,561 (GRCm39)	missense	probably benign
R5901:Tmem39a	UTSW	16	38,393,568 (GRCm39)	missense	probably benign	0.00
R5978:Tmem39a	UTSW	16	38,411,392 (GRCm39)	missense	probably benign	0.12
R5979:Tmem39a	UTSW	16	38,396,106 (GRCm39)	missense	probably damaging	0.99
R6375:Tmem39a	UTSW	16	38,405,599 (GRCm39)	missense	probably benign	0.00
R7357:Tmem39a	UTSW	16	38,406,592 (GRCm39)	missense	probably damaging	1.00
R7485:Tmem39a	UTSW	16	38,408,658 (GRCm39)	missense	possibly damaging	0.51
R8114:Tmem39a	UTSW	16	38,411,359 (GRCm39)	missense	probably damaging	1.00
R8114:Tmem39a	UTSW	16	38,411,358 (GRCm39)	missense	probably damaging	1.00
R9756:Tmem39a	UTSW	16	38,396,126 (GRCm39)	missense	probably benign
Z1088:Tmem39a	UTSW	16	38,396,140 (GRCm39)	missense	possibly damaging	0.69
Z1176:Tmem39a	UTSW	16	38,408,586 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- TTCTAGATCTCTACAGCAAGGATAG -3'
(R):5'- ATCTGAATTCTCCCTCCTGTTGAGAG -3'

Sequencing Primer
(F):5'- GGATAGTTTGCCACTAAATATGCAG -3'
(R):5'- CCTCCTGTTGAGAGACAGCTTAG -3'

Posted On

2016-06-15