Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL01935:Rapgef6'

180603

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Rapgef6

Ensembl Gene

ENSMUSG00000037533

Gene Name

Rap guanine nucleotide exchange factor (GEF) 6

Synonyms

PDZ-GEF2, C030018K18Rik, Pdzgef2, RA-GEF-2

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

IGL01935

Quality Score

Status

Chromosome

Chromosomal Location

54413673-54590111 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 54501668 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 184 (T184A)

Ref Sequence

ENSEMBL: ENSMUSP00000099804 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000101206] [ENSMUST00000102743] [ENSMUST00000108895] [ENSMUST00000207429] [ENSMUST00000218995]

AlphaFold

Q5NCJ1

Predicted Effect

possibly damaging
Transcript: ENSMUST00000101206
AA Change: T184A

PolyPhen 2 Score 0.777 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000098766
Gene: ENSMUSG00000037533
AA Change: T184A

Domain	Start	End	E-Value	Type
internal_repeat_1	10	82	1.45e-5	PROSPERO
low complexity region	187	205	N/A	INTRINSIC
low complexity region	231	239	N/A	INTRINSIC
cNMP	280	398	4.8e-13	SMART
RasGEFN	412	525	4.35e-33	SMART
PDZ	540	612	8.86e-16	SMART
low complexity region	694	705	N/A	INTRINSIC
RA	749	835	1.47e-20	SMART
RasGEF	856	1095	5.35e-87	SMART
low complexity region	1237	1250	N/A	INTRINSIC
low complexity region	1270	1293	N/A	INTRINSIC
low complexity region	1345	1364	N/A	INTRINSIC
low complexity region	1368	1380	N/A	INTRINSIC
low complexity region	1444	1452	N/A	INTRINSIC
low complexity region	1555	1568	N/A	INTRINSIC
low complexity region	1591	1604	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000102743
AA Change: T184A

PolyPhen 2 Score 0.777 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000099804
Gene: ENSMUSG00000037533
AA Change: T184A

Domain	Start	End	E-Value	Type
internal_repeat_1	10	82	1.42e-5	PROSPERO
low complexity region	187	205	N/A	INTRINSIC
low complexity region	231	239	N/A	INTRINSIC
cNMP	280	398	4.8e-13	SMART
RasGEFN	412	525	4.35e-33	SMART
PDZ	540	612	8.86e-16	SMART
low complexity region	694	705	N/A	INTRINSIC
RA	749	835	1.47e-20	SMART
RasGEF	856	1138	3.88e-84	SMART
low complexity region	1229	1242	N/A	INTRINSIC
low complexity region	1262	1285	N/A	INTRINSIC
low complexity region	1337	1356	N/A	INTRINSIC
low complexity region	1360	1372	N/A	INTRINSIC
low complexity region	1436	1444	N/A	INTRINSIC
low complexity region	1547	1560	N/A	INTRINSIC
low complexity region	1583	1596	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000108895
AA Change: T184A

PolyPhen 2 Score 0.022 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000104523
Gene: ENSMUSG00000037533
AA Change: T184A

Domain	Start	End	E-Value	Type
internal_repeat_1	10	82	1.95e-5	PROSPERO
low complexity region	187	205	N/A	INTRINSIC
low complexity region	231	239	N/A	INTRINSIC
cNMP	280	398	4.8e-13	SMART
RasGEFN	412	526	1.03e-25	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149372

Predicted Effect

probably benign
Transcript: ENSMUST00000207429
AA Change: T184A

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)

Predicted Effect

probably benign
Transcript: ENSMUST00000218995
AA Change: T37A

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000220269

Coding Region Coverage

Validation Efficiency

MGI Phenotype

PHENOTYPE: Mice homozygous for a null allele exhibit an inlarged spleen, increased IgE and IgG levels and altered cytokine production. [provided by MGI curators]

Allele List at MGI

All alleles(16) : Targeted, knock-out(1) Targeted, other(2) Gene trapped(13)

Other mutations in this stock

Total: 55 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aebp2	C	T	6: 140,583,383 (GRCm39)		probably benign	Het
Akr1c12	A	T	13: 4,322,244 (GRCm39)	V266E	probably damaging	Het
Arhgef1	A	G	7: 24,621,307 (GRCm39)	T186A	probably damaging	Het
Atp8b5	A	G	4: 43,366,638 (GRCm39)	T801A	probably benign	Het
Card11	T	A	5: 140,869,301 (GRCm39)	I832F	possibly damaging	Het
Catsperg1	T	C	7: 28,895,296 (GRCm39)		probably null	Het
Ccdc180	A	G	4: 45,906,889 (GRCm39)	T455A	possibly damaging	Het
Cfhr1	T	A	1: 139,478,740 (GRCm39)	Y210F	probably benign	Het
Chrna5	T	C	9: 54,912,127 (GRCm39)	V309A	probably benign	Het
Clstn2	A	G	9: 97,345,521 (GRCm39)	V609A	probably damaging	Het
Dnah6	T	C	6: 73,037,126 (GRCm39)	D3372G	probably benign	Het
Dtymk	T	C	1: 93,722,465 (GRCm39)	K113E	probably benign	Het
Eef2k	T	C	7: 120,485,054 (GRCm39)	F307S	probably damaging	Het
Flnc	T	A	6: 29,454,279 (GRCm39)	V1864E	probably damaging	Het
Gm10717	C	T	9: 3,025,616 (GRCm39)	S67L	probably benign	Het
Herc2	A	G	7: 55,803,541 (GRCm39)	Y2192C	probably benign	Het
Hkdc1	A	T	10: 62,236,165 (GRCm39)	V459E	probably damaging	Het
Iqsec3	T	C	6: 121,360,951 (GRCm39)	D969G	probably damaging	Het
Irf3	A	G	7: 44,650,194 (GRCm39)	T237A	probably benign	Het
Jade2	G	A	11: 51,719,211 (GRCm39)	T245I	possibly damaging	Het
Kctd8	A	G	5: 69,497,707 (GRCm39)	I313T	possibly damaging	Het
Kdm5a	T	A	6: 120,385,284 (GRCm39)	S835R	probably benign	Het
Lama2	A	C	10: 27,298,600 (GRCm39)	H165Q	probably damaging	Het
Lrp1b	T	A	2: 41,158,367 (GRCm39)	N1617Y	probably damaging	Het
Mcc	C	T	18: 44,652,583 (GRCm39)		probably null	Het
Mfsd14b	T	A	13: 65,215,739 (GRCm39)	M405L	probably benign	Het
Myom3	T	A	4: 135,515,692 (GRCm39)	F794I	probably damaging	Het
Napsa	G	T	7: 44,236,046 (GRCm39)	A362S	probably benign	Het
Ncf4	A	T	15: 78,140,186 (GRCm39)	D195V	probably damaging	Het
Or11g1	T	C	14: 50,651,012 (GRCm39)	F4L	probably benign	Het
Pank4	T	G	4: 155,063,987 (GRCm39)	D659E	probably damaging	Het
Pcnx1	T	A	12: 81,964,590 (GRCm39)	D252E	probably benign	Het
Pglyrp2	G	A	17: 32,637,551 (GRCm39)	A159V	probably benign	Het
Phaf1	T	C	8: 105,966,633 (GRCm39)	F127L	probably damaging	Het
Pisd	C	A	5: 32,896,476 (GRCm39)		probably null	Het
Ppfia4	A	G	1: 134,245,674 (GRCm39)	S627P	probably benign	Het
Ppp1r15b	T	C	1: 133,059,761 (GRCm39)	F93L	probably benign	Het
Pramel13	C	T	4: 144,119,172 (GRCm39)		probably benign	Het
Qrfpr	A	T	3: 36,235,200 (GRCm39)		probably null	Het
Rapgef4	C	A	2: 72,064,467 (GRCm39)	T623K	probably benign	Het
Ssrp1	T	C	2: 84,877,056 (GRCm39)	*709Q	probably null	Het
St7	T	G	6: 17,930,822 (GRCm39)	I442S	probably damaging	Het
Syne2	T	A	12: 75,972,087 (GRCm39)	H992Q	probably damaging	Het
Syt14	T	C	1: 192,615,679 (GRCm39)	R436G	probably damaging	Het
Tbc1d5	A	G	17: 51,270,793 (GRCm39)		probably benign	Het
Thsd7a	T	A	6: 12,317,418 (GRCm39)	N1630I	probably damaging	Het
Tinagl1	T	C	4: 130,061,794 (GRCm39)	K180R	probably damaging	Het
Tmed7	T	C	18: 46,730,190 (GRCm39)	T54A	probably benign	Het
Tmprss2	A	T	16: 97,379,795 (GRCm39)	Y48*	probably null	Het
Tns2	C	T	15: 102,020,069 (GRCm39)		probably null	Het
Unc13d	T	C	11: 115,960,577 (GRCm39)	M496V	probably benign	Het
Vmn2r129	C	T	4: 156,690,549 (GRCm39)		noncoding transcript	Het
Zbtb39	A	G	10: 127,578,235 (GRCm39)	T270A	probably benign	Het
Zfr	T	C	15: 12,180,798 (GRCm39)	S976P	probably benign	Het
Zscan29	A	G	2: 121,000,538 (GRCm39)	F23S	probably damaging	Het

Other mutations in Rapgef6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00436:Rapgef6	APN	11	54,570,091 (GRCm39)	missense	probably benign	0.00
IGL00507:Rapgef6	APN	11	54,554,935 (GRCm39)	nonsense	probably null
IGL00809:Rapgef6	APN	11	54,540,126 (GRCm39)	missense	probably damaging	1.00
IGL00843:Rapgef6	APN	11	54,582,099 (GRCm39)	missense	probably benign	0.03
IGL00899:Rapgef6	APN	11	54,510,844 (GRCm39)	nonsense	probably null
IGL01372:Rapgef6	APN	11	54,559,437 (GRCm39)	splice site	probably benign
IGL01604:Rapgef6	APN	11	54,585,389 (GRCm39)	missense	probably damaging	0.99
IGL01991:Rapgef6	APN	11	54,443,695 (GRCm39)	missense	probably benign	0.37
IGL02243:Rapgef6	APN	11	54,567,226 (GRCm39)	missense	probably damaging	1.00
IGL02407:Rapgef6	APN	11	54,567,181 (GRCm39)	missense	possibly damaging	0.91
IGL02676:Rapgef6	APN	11	54,540,172 (GRCm39)	unclassified	probably benign
IGL02934:Rapgef6	APN	11	54,516,690 (GRCm39)	missense	probably damaging	1.00
IGL03076:Rapgef6	APN	11	54,516,793 (GRCm39)	missense	probably damaging	1.00
IGL03110:Rapgef6	APN	11	54,586,915 (GRCm39)	missense	probably damaging	0.97
IGL03256:Rapgef6	APN	11	54,548,255 (GRCm39)	missense	probably damaging	1.00
shocker	UTSW	11	54,510,842 (GRCm39)	missense	probably damaging	1.00
D4216:Rapgef6	UTSW	11	54,559,572 (GRCm39)	splice site	probably benign
PIT4305001:Rapgef6	UTSW	11	54,570,203 (GRCm39)	missense	probably damaging	1.00
PIT4366001:Rapgef6	UTSW	11	54,582,446 (GRCm39)	missense	probably damaging	0.98
R0047:Rapgef6	UTSW	11	54,437,204 (GRCm39)	missense	possibly damaging	0.65
R0047:Rapgef6	UTSW	11	54,437,204 (GRCm39)	missense	possibly damaging	0.65
R0125:Rapgef6	UTSW	11	54,516,701 (GRCm39)	nonsense	probably null
R0189:Rapgef6	UTSW	11	54,582,075 (GRCm39)	missense	probably benign
R0201:Rapgef6	UTSW	11	54,510,767 (GRCm39)	missense	probably damaging	1.00
R0505:Rapgef6	UTSW	11	54,516,789 (GRCm39)	missense	probably benign	0.00
R0524:Rapgef6	UTSW	11	54,581,110 (GRCm39)	missense	probably benign	0.32
R0853:Rapgef6	UTSW	11	54,559,503 (GRCm39)	missense	probably damaging	1.00
R1203:Rapgef6	UTSW	11	54,582,525 (GRCm39)	missense	probably benign	0.09
R1440:Rapgef6	UTSW	11	54,517,534 (GRCm39)	missense	probably damaging	1.00
R1453:Rapgef6	UTSW	11	54,530,553 (GRCm39)	splice site	probably null
R1530:Rapgef6	UTSW	11	54,552,009 (GRCm39)	missense	probably damaging	1.00
R1593:Rapgef6	UTSW	11	54,437,223 (GRCm39)	frame shift	probably null
R1620:Rapgef6	UTSW	11	54,517,420 (GRCm39)	missense	possibly damaging	0.88
R1628:Rapgef6	UTSW	11	54,437,223 (GRCm39)	frame shift	probably null
R1629:Rapgef6	UTSW	11	54,437,223 (GRCm39)	frame shift	probably null
R1630:Rapgef6	UTSW	11	54,437,223 (GRCm39)	frame shift	probably null
R1634:Rapgef6	UTSW	11	54,437,223 (GRCm39)	frame shift	probably null
R1640:Rapgef6	UTSW	11	54,548,231 (GRCm39)	missense	probably damaging	1.00
R1686:Rapgef6	UTSW	11	54,582,458 (GRCm39)	missense	possibly damaging	0.81
R1722:Rapgef6	UTSW	11	54,437,223 (GRCm39)	frame shift	probably null
R1743:Rapgef6	UTSW	11	54,567,110 (GRCm39)	missense	probably damaging	1.00
R1816:Rapgef6	UTSW	11	54,585,314 (GRCm39)	missense	probably benign
R1851:Rapgef6	UTSW	11	54,533,637 (GRCm39)	missense	probably benign	0.01
R1852:Rapgef6	UTSW	11	54,533,637 (GRCm39)	missense	probably benign	0.01
R1868:Rapgef6	UTSW	11	54,437,223 (GRCm39)	frame shift	probably null
R1888:Rapgef6	UTSW	11	54,551,654 (GRCm39)	missense	probably damaging	1.00
R1888:Rapgef6	UTSW	11	54,551,654 (GRCm39)	missense	probably damaging	1.00
R1942:Rapgef6	UTSW	11	54,548,089 (GRCm39)	missense	possibly damaging	0.95
R1943:Rapgef6	UTSW	11	54,548,089 (GRCm39)	missense	possibly damaging	0.95
R2031:Rapgef6	UTSW	11	54,443,684 (GRCm39)	missense	probably benign	0.30
R2087:Rapgef6	UTSW	11	54,522,075 (GRCm39)	missense	probably damaging	1.00
R2106:Rapgef6	UTSW	11	54,559,512 (GRCm39)	missense	probably benign	0.17
R2362:Rapgef6	UTSW	11	54,585,098 (GRCm39)	missense	probably damaging	1.00
R2484:Rapgef6	UTSW	11	54,533,582 (GRCm39)	missense	possibly damaging	0.48
R2566:Rapgef6	UTSW	11	54,578,537 (GRCm39)	missense	possibly damaging	0.66
R2872:Rapgef6	UTSW	11	54,552,001 (GRCm39)	missense	probably damaging	1.00
R2872:Rapgef6	UTSW	11	54,552,001 (GRCm39)	missense	probably damaging	1.00
R3744:Rapgef6	UTSW	11	54,516,760 (GRCm39)	missense	probably benign	0.40
R3848:Rapgef6	UTSW	11	54,582,134 (GRCm39)	missense	probably damaging	0.97
R4823:Rapgef6	UTSW	11	54,585,326 (GRCm39)	missense	probably benign	0.08
R4859:Rapgef6	UTSW	11	54,526,989 (GRCm39)	missense	probably benign
R4906:Rapgef6	UTSW	11	54,443,662 (GRCm39)	missense	probably damaging	1.00
R4911:Rapgef6	UTSW	11	54,513,143 (GRCm39)	missense	probably damaging	0.97
R4937:Rapgef6	UTSW	11	54,548,143 (GRCm39)	missense	probably damaging	1.00
R5033:Rapgef6	UTSW	11	54,582,207 (GRCm39)	missense	possibly damaging	0.92
R5249:Rapgef6	UTSW	11	54,413,943 (GRCm39)	missense	probably benign	0.19
R5304:Rapgef6	UTSW	11	54,548,200 (GRCm39)	missense	probably benign	0.01
R5656:Rapgef6	UTSW	11	54,526,962 (GRCm39)	missense	possibly damaging	0.95
R5701:Rapgef6	UTSW	11	54,567,220 (GRCm39)	missense	possibly damaging	0.76
R5758:Rapgef6	UTSW	11	54,559,470 (GRCm39)	missense	probably damaging	1.00
R5973:Rapgef6	UTSW	11	54,530,609 (GRCm39)	missense	probably damaging	1.00
R6177:Rapgef6	UTSW	11	54,510,842 (GRCm39)	missense	probably damaging	1.00
R6268:Rapgef6	UTSW	11	54,540,073 (GRCm39)	missense	probably damaging	1.00
R6287:Rapgef6	UTSW	11	54,517,164 (GRCm39)	splice site	probably null
R6293:Rapgef6	UTSW	11	54,525,607 (GRCm39)	missense	probably damaging	1.00
R6471:Rapgef6	UTSW	11	54,582,563 (GRCm39)	missense	probably damaging	0.99
R6863:Rapgef6	UTSW	11	54,437,206 (GRCm39)	missense	probably benign	0.00
R6950:Rapgef6	UTSW	11	54,567,206 (GRCm39)	missense	probably benign	0.09
R7144:Rapgef6	UTSW	11	54,548,191 (GRCm39)	missense	possibly damaging	0.78
R7171:Rapgef6	UTSW	11	54,567,189 (GRCm39)	missense	possibly damaging	0.94
R7199:Rapgef6	UTSW	11	54,437,252 (GRCm39)	missense	probably benign	0.00
R7291:Rapgef6	UTSW	11	54,582,065 (GRCm39)	missense	probably benign	0.05
R7436:Rapgef6	UTSW	11	54,501,747 (GRCm39)	critical splice donor site	probably null
R7498:Rapgef6	UTSW	11	54,510,830 (GRCm39)	missense	probably damaging	1.00
R7506:Rapgef6	UTSW	11	54,526,997 (GRCm39)	missense	probably benign	0.00
R7527:Rapgef6	UTSW	11	54,525,787 (GRCm39)	missense	unknown
R7646:Rapgef6	UTSW	11	54,516,780 (GRCm39)	missense	probably benign	0.00
R7655:Rapgef6	UTSW	11	54,585,279 (GRCm39)	missense	probably benign	0.10
R7656:Rapgef6	UTSW	11	54,585,279 (GRCm39)	missense	probably benign	0.10
R7687:Rapgef6	UTSW	11	54,551,901 (GRCm39)	missense	possibly damaging	0.93
R7768:Rapgef6	UTSW	11	54,517,414 (GRCm39)	missense	probably damaging	1.00
R7788:Rapgef6	UTSW	11	54,585,225 (GRCm39)	missense	probably damaging	1.00
R7890:Rapgef6	UTSW	11	54,517,549 (GRCm39)	missense	probably damaging	1.00
R8113:Rapgef6	UTSW	11	54,516,784 (GRCm39)	missense	probably benign	0.03
R8337:Rapgef6	UTSW	11	54,522,127 (GRCm39)	nonsense	probably null
R8393:Rapgef6	UTSW	11	54,578,487 (GRCm39)	missense	probably benign
R8465:Rapgef6	UTSW	11	54,582,308 (GRCm39)	missense	probably benign	0.00
R8492:Rapgef6	UTSW	11	54,581,063 (GRCm39)	missense	probably damaging	0.99
R8791:Rapgef6	UTSW	11	54,459,295 (GRCm39)	missense	probably benign	0.15
R8866:Rapgef6	UTSW	11	54,443,700 (GRCm39)	critical splice donor site	probably null
R8917:Rapgef6	UTSW	11	54,582,392 (GRCm39)	nonsense	probably null
R8921:Rapgef6	UTSW	11	54,570,065 (GRCm39)	missense	probably benign	0.09
R9031:Rapgef6	UTSW	11	54,578,667 (GRCm39)	missense	probably benign	0.00
R9093:Rapgef6	UTSW	11	54,487,912 (GRCm39)	nonsense	probably null
R9354:Rapgef6	UTSW	11	54,510,749 (GRCm39)	missense	possibly damaging	0.66
R9514:Rapgef6	UTSW	11	54,443,684 (GRCm39)	missense	probably benign	0.14
R9516:Rapgef6	UTSW	11	54,582,169 (GRCm39)	missense	probably damaging	1.00
R9739:Rapgef6	UTSW	11	54,513,189 (GRCm39)	missense	probably benign	0.03
R9789:Rapgef6	UTSW	11	54,540,097 (GRCm39)	missense	probably benign	0.03

Posted On

2014-05-07