Mutagenetix > Incidental Mutation

Incidental Mutation 'R3977:Raph1'

311051

Institutional Source

Beutler Lab

Gene Symbol

Raph1

Ensembl Gene

ENSMUSG00000026014

Gene Name

Ras association (RalGDS/AF-6) and pleckstrin homology domains 1

Synonyms

C730009O10Rik, Lpd, 9430025M21Rik, lamellipodin

MMRRC Submission

040940-MU

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.117) question?

Stock #

R3977 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

60482292-60567104 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 60498523 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 491 (D491E)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000027168] [ENSMUST00000090293] [ENSMUST00000140485]

AlphaFold

F2Z3U3

Predicted Effect

probably benign
Transcript: ENSMUST00000027168
AA Change: D491E

PolyPhen 2 Score 0.164 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000027168
Gene: ENSMUSG00000026014
AA Change: D491E

Domain	Start	End	E-Value	Type
low complexity region	201	218	N/A	INTRINSIC
low complexity region	294	308	N/A	INTRINSIC
RA	322	408	1.63e-13	SMART
PH	450	560	3.38e-11	SMART
low complexity region	581	604	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000090293
AA Change: D491E

PolyPhen 2 Score 0.095 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000087763
Gene: ENSMUSG00000026014
AA Change: D491E

Domain	Start	End	E-Value	Type
low complexity region	201	218	N/A	INTRINSIC
low complexity region	294	308	N/A	INTRINSIC
RA	322	408	1.63e-13	SMART
PH	450	560	3.38e-11	SMART
low complexity region	581	604	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000127573
AA Change: D491E

PolyPhen 2 Score 0.394 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000114596
Gene: ENSMUSG00000026014
AA Change: D491E

Domain	Start	End	E-Value	Type
low complexity region	201	218	N/A	INTRINSIC
coiled coil region	295	320	N/A	INTRINSIC
RA	322	408	1e-15	SMART
PH	450	560	1.6e-13	SMART
low complexity region	581	604	N/A	INTRINSIC
low complexity region	656	661	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000140485
AA Change: D439E

SMART Domains

Protein: ENSMUSP00000121023
Gene: ENSMUSG00000026014
AA Change: D439E

Domain	Start	End	E-Value	Type
low complexity region	201	218	N/A	INTRINSIC
low complexity region	245	256	N/A	INTRINSIC
RA	270	356	1.63e-13	SMART
PH	398	508	3.38e-11	SMART
low complexity region	529	552	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000182085
AA Change: D27E

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000188511

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000189383

Meta Mutation Damage Score

0.2499

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.9%
20x: 93.7%

Validation Efficiency

96% (50/52)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that belongs to the Mig10/Rap1-interacting adaptor molecule/Lamellipodin family of adapter proteins, which function in cell migration. Members of this family contain pleckstrin-homology domains, Ras-association domains, and proline-rich C-termini. The protein encoded by this gene regulates actin dynamics through interaction with Ena/Vasodilator proteins as well as direct binding to filamentous actin to regulate actin network assembly. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]
PHENOTYPE: Mice homozygous for a conditional allele activated in all cells exhibit background sensitive neonatal or postnatal lethality, decreased body size, belly spotting and decreased melanocyte numbers in the trunk. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ace	C	T	11: 105,981,838	P942L	possibly damaging	Het
Adam28	A	G	14: 68,610,994	V671A	probably benign	Het
Arfgef1	A	G	1: 10,209,634	V236A	probably benign	Het
B020004C17Rik	G	T	14: 57,017,188	M156I	possibly damaging	Het
Bicral	T	A	17: 46,830,991	M1L	unknown	Het
Brpf3	A	G	17: 28,807,042	E363G	possibly damaging	Het
Ccdc96	T	C	5: 36,485,166	L172P	possibly damaging	Het
Cln3	G	A	7: 126,580,136		probably benign	Het
Dnah7c	T	C	1: 46,628,911	I1526T	possibly damaging	Het
Fmo3	T	G	1: 162,958,578	E281A	probably damaging	Het
Frem2	A	G	3: 53,652,070	I1672T	probably benign	Het
Gbp2b	A	G	3: 142,603,709	I194V	probably benign	Het
Gprc6a	C	A	10: 51,621,101	V449L	probably benign	Het
Hk1	A	G	10: 62,290,319	V396A	probably benign	Het
Hoxc13	T	C	15: 102,921,240	V18A	possibly damaging	Het
Hr	A	G	14: 70,563,584	T699A	probably benign	Het
Il19	A	T	1: 130,936,033	C74S	probably damaging	Het
Krt2	T	C	15: 101,811,127	T703A	unknown	Het
Lrig2	A	T	3: 104,457,844	V664E	probably damaging	Het
Lrrc37a	T	C	11: 103,457,604	K2755R	unknown	Het
Man1c1	G	C	4: 134,703,438	P11R	probably damaging	Het
Mbtd1	A	G	11: 93,905,175	N13D	probably benign	Het
Mfsd4b5	T	C	10: 39,974,708		probably benign	Het
Nras	A	G	3: 103,060,225	I46V	probably benign	Het
Oasl1	C	T	5: 114,932,898	T274I	probably damaging	Het
Ogfod2	C	A	5: 124,113,209		probably null	Het
Olfr1264	C	A	2: 90,021,745	G107V	probably damaging	Het
Olfr1369-ps1	T	A	13: 21,115,861	H56Q	probably benign	Het
Olfr1419	C	A	19: 11,870,505	R237L	possibly damaging	Het
Olfr1420	T	A	19: 11,896,516	F165Y	probably damaging	Het
Olfr774	C	T	10: 129,238,508	R120C	probably damaging	Het
Olfr96	T	C	17: 37,225,158	V11A	probably benign	Het
Pkmyt1	A	G	17: 23,735,331	M362V	probably benign	Het
Ppfia2	A	G	10: 106,830,629	T399A	possibly damaging	Het
Ppp1r12b	A	G	1: 134,765,975	S983P	probably benign	Het
Ptpn22	A	G	3: 103,873,641		probably benign	Het
Rc3h1	A	G	1: 160,959,399		probably null	Het
Rtn4	T	C	11: 29,693,819	L5P	probably benign	Het
Sdccag3	T	A	2: 26,384,793	N364I	probably damaging	Het
Slc23a4	C	T	6: 34,953,788	V400I	probably benign	Het
Slco1a5	A	G	6: 142,258,972		probably benign	Het
Smpd1	T	C	7: 105,555,901	F329S	probably benign	Het
Sycp2l	A	G	13: 41,141,964	I334M	probably damaging	Het
Tas2r103	A	G	6: 133,036,317	L262P	probably benign	Het
Ten1	G	A	11: 116,216,945		probably null	Het
Tfap2d	C	G	1: 19,104,494	S57C	possibly damaging	Het
Tnr	A	G	1: 159,892,023	M957V	probably benign	Het
Trbv13-3	A	G	6: 41,130,145		probably benign	Het
Trp53rkb	C	T	2: 166,795,526	A134V	possibly damaging	Het
Trp63	A	G	16: 25,820,740		probably benign	Het
Vmn2r112	T	A	17: 22,603,115	V258E	probably damaging	Het
Vmn2r74	T	C	7: 85,958,137	Y126C	probably benign	Het
Vmn2r96	T	A	17: 18,597,679	I698N	probably damaging	Het

Other mutations in Raph1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02300:Raph1	APN	1	60525947	missense	possibly damaging	0.76
IGL02900:Raph1	APN	1	60502863	missense	probably damaging	1.00
FR4976:Raph1	UTSW	1	60489267	intron	probably benign
R0048:Raph1	UTSW	1	60500605	missense	probably benign	0.03
R0048:Raph1	UTSW	1	60500605	missense	probably benign	0.03
R0049:Raph1	UTSW	1	60525899	missense	probably benign	0.03
R0049:Raph1	UTSW	1	60525899	missense	probably benign	0.03
R0227:Raph1	UTSW	1	60525977	missense	probably benign	0.00
R0387:Raph1	UTSW	1	60510496	intron	probably benign
R0607:Raph1	UTSW	1	60525869	missense	probably damaging	1.00
R1740:Raph1	UTSW	1	60519024	nonsense	probably null
R2274:Raph1	UTSW	1	60498500	missense	probably damaging	1.00
R3108:Raph1	UTSW	1	60493386	missense	probably benign	0.01
R4260:Raph1	UTSW	1	60502965	missense	possibly damaging	0.94
R4487:Raph1	UTSW	1	60502869	missense	possibly damaging	0.68
R4721:Raph1	UTSW	1	60503001	unclassified	probably benign
R4782:Raph1	UTSW	1	60489114	missense	probably damaging	1.00
R5027:Raph1	UTSW	1	60496277	missense	probably damaging	1.00
R5037:Raph1	UTSW	1	60496222	splice site	probably null
R5106:Raph1	UTSW	1	60533300	missense	probably damaging	1.00
R5506:Raph1	UTSW	1	60493498	intron	probably benign
R5510:Raph1	UTSW	1	60522946	unclassified	probably benign
R5587:Raph1	UTSW	1	60498473	missense	probably damaging	1.00
R5591:Raph1	UTSW	1	60501746	unclassified	probably benign
R5619:Raph1	UTSW	1	60490255	intron	probably benign
R5776:Raph1	UTSW	1	60490156	intron	probably benign
R5802:Raph1	UTSW	1	60488673	missense	possibly damaging	0.81
R6742:Raph1	UTSW	1	60525720	missense	probably damaging	0.97
R7122:Raph1	UTSW	1	60525977	missense	probably benign	0.10
R7219:Raph1	UTSW	1	60502873	missense	unknown
R7251:Raph1	UTSW	1	60489868	missense	unknown
R7254:Raph1	UTSW	1	60499608	missense	unknown
R7732:Raph1	UTSW	1	60533288	missense	possibly damaging	0.82
R7979:Raph1	UTSW	1	60525989	missense	probably benign	0.00
R7986:Raph1	UTSW	1	60496286	missense
R8167:Raph1	UTSW	1	60490111	missense	unknown
R8168:Raph1	UTSW	1	60499620	missense	unknown
R8399:Raph1	UTSW	1	60489318	missense	unknown
R9036:Raph1	UTSW	1	60502965	missense	unknown
R9146:Raph1	UTSW	1	60518978	critical splice donor site	probably null
R9338:Raph1	UTSW	1	60490141	missense	unknown
R9381:Raph1	UTSW	1	60501800	missense	unknown
R9383:Raph1	UTSW	1	60525670	missense	unknown
R9399:Raph1	UTSW	1	60525995	missense	probably benign
R9454:Raph1	UTSW	1	60489594	missense	unknown
R9561:Raph1	UTSW	1	60525728	missense	possibly damaging	0.49
RF018:Raph1	UTSW	1	60489267	intron	probably benign
RF022:Raph1	UTSW	1	60489267	intron	probably benign

Predicted Primers

PCR Primer
(F):5'- TCCCTGGTACTACAGATGAAGC -3'
(R):5'- GCAAAATGGACTGCTCTTTTGGTTAC -3'

Sequencing Primer
(F):5'- TGAAGCTAAAATGCTAGGGTTACCCC -3'
(R):5'- ACTGCTCTTTTGGTTACATTGTAGAC -3'

Posted On

2015-04-29