Mutagenetix > Incidental Mutation

Incidental Mutation 'R4584:Phc3'

343894

Institutional Source

Beutler Lab

Gene Symbol

Phc3

Ensembl Gene

ENSMUSG00000037652

Gene Name

polyhomeotic 3

Synonyms

EDR3, E030046K01Rik, HPH3

MMRRC Submission

041805-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4584 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

30953520-31023564 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 31020031 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 23 (V23A)

Ref Sequence

ENSEMBL: ENSMUSP00000117614 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000046624] [ENSMUST00000064718] [ENSMUST00000099163] [ENSMUST00000108255] [ENSMUST00000129817] [ENSMUST00000152357] [ENSMUST00000168645] [ENSMUST00000177992]

AlphaFold

Q8CHP6

Predicted Effect

possibly damaging
Transcript: ENSMUST00000046624
AA Change: V23A

PolyPhen 2 Score 0.455 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000037862
Gene: ENSMUSG00000037652
AA Change: V23A

Domain	Start	End	E-Value	Type
low complexity region	18	40	N/A	INTRINSIC
low complexity region	72	89	N/A	INTRINSIC
low complexity region	92	142	N/A	INTRINSIC
low complexity region	152	166	N/A	INTRINSIC
low complexity region	206	224	N/A	INTRINSIC
low complexity region	333	359	N/A	INTRINSIC
low complexity region	393	419	N/A	INTRINSIC
low complexity region	512	538	N/A	INTRINSIC
low complexity region	564	578	N/A	INTRINSIC
low complexity region	583	594	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000064718
AA Change: V23A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000065617
Gene: ENSMUSG00000037652
AA Change: V23A

Domain	Start	End	E-Value	Type
low complexity region	18	40	N/A	INTRINSIC
low complexity region	72	89	N/A	INTRINSIC
low complexity region	92	142	N/A	INTRINSIC
low complexity region	152	166	N/A	INTRINSIC
low complexity region	206	224	N/A	INTRINSIC
low complexity region	333	359	N/A	INTRINSIC
low complexity region	393	419	N/A	INTRINSIC
low complexity region	470	496	N/A	INTRINSIC
low complexity region	522	536	N/A	INTRINSIC
low complexity region	541	571	N/A	INTRINSIC
low complexity region	610	618	N/A	INTRINSIC
low complexity region	628	656	N/A	INTRINSIC
PDB:2L8E\|A	745	781	1e-8	PDB
low complexity region	849	868	N/A	INTRINSIC
SAM	884	951	4.04e-13	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000099163
AA Change: V23A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000096767
Gene: ENSMUSG00000037652
AA Change: V23A

Domain	Start	End	E-Value	Type
low complexity region	18	40	N/A	INTRINSIC
low complexity region	72	89	N/A	INTRINSIC
low complexity region	92	142	N/A	INTRINSIC
low complexity region	152	166	N/A	INTRINSIC
low complexity region	300	326	N/A	INTRINSIC
low complexity region	360	386	N/A	INTRINSIC
low complexity region	479	505	N/A	INTRINSIC
low complexity region	531	545	N/A	INTRINSIC
low complexity region	550	580	N/A	INTRINSIC
low complexity region	619	627	N/A	INTRINSIC
low complexity region	637	665	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000108255
AA Change: V11A

PolyPhen 2 Score 0.326 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000103890
Gene: ENSMUSG00000037652
AA Change: V11A

Domain	Start	End	E-Value	Type
low complexity region	6	28	N/A	INTRINSIC
low complexity region	60	77	N/A	INTRINSIC
low complexity region	80	130	N/A	INTRINSIC
low complexity region	140	154	N/A	INTRINSIC
low complexity region	288	314	N/A	INTRINSIC
low complexity region	348	374	N/A	INTRINSIC
low complexity region	467	493	N/A	INTRINSIC
low complexity region	519	533	N/A	INTRINSIC
low complexity region	538	568	N/A	INTRINSIC
low complexity region	607	615	N/A	INTRINSIC
low complexity region	625	653	N/A	INTRINSIC
PDB:2L8E\|A	742	778	8e-9	PDB
low complexity region	846	865	N/A	INTRINSIC
SAM	881	948	4.04e-13	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000129817
AA Change: V11A

PolyPhen 2 Score 0.326 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000114916
Gene: ENSMUSG00000037652
AA Change: V11A

Domain	Start	End	E-Value	Type
low complexity region	6	28	N/A	INTRINSIC
low complexity region	60	77	N/A	INTRINSIC
low complexity region	80	130	N/A	INTRINSIC
low complexity region	140	154	N/A	INTRINSIC
low complexity region	194	212	N/A	INTRINSIC
low complexity region	321	347	N/A	INTRINSIC
low complexity region	381	407	N/A	INTRINSIC
low complexity region	500	526	N/A	INTRINSIC
low complexity region	552	566	N/A	INTRINSIC
low complexity region	571	601	N/A	INTRINSIC
low complexity region	640	648	N/A	INTRINSIC
low complexity region	658	686	N/A	INTRINSIC
PDB:2L8E\|A	775	811	7e-9	PDB
low complexity region	879	898	N/A	INTRINSIC
SAM	914	980	1.7e-11	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000150939

Predicted Effect

possibly damaging
Transcript: ENSMUST00000152357
AA Change: V23A

PolyPhen 2 Score 0.455 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000117614
Gene: ENSMUSG00000037652
AA Change: V23A

Domain	Start	End	E-Value	Type
low complexity region	18	40	N/A	INTRINSIC
low complexity region	72	89	N/A	INTRINSIC
low complexity region	92	142	N/A	INTRINSIC
low complexity region	152	166	N/A	INTRINSIC
low complexity region	201	222	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000168645
AA Change: V11A

PolyPhen 2 Score 0.326 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000130142
Gene: ENSMUSG00000037652
AA Change: V11A

Domain	Start	End	E-Value	Type
low complexity region	6	28	N/A	INTRINSIC
low complexity region	60	77	N/A	INTRINSIC
low complexity region	80	130	N/A	INTRINSIC
low complexity region	140	154	N/A	INTRINSIC
low complexity region	194	212	N/A	INTRINSIC
low complexity region	321	347	N/A	INTRINSIC
low complexity region	381	407	N/A	INTRINSIC
low complexity region	500	526	N/A	INTRINSIC
low complexity region	552	566	N/A	INTRINSIC
low complexity region	571	601	N/A	INTRINSIC
low complexity region	640	648	N/A	INTRINSIC
low complexity region	658	686	N/A	INTRINSIC
PDB:2L8E\|A	775	811	7e-9	PDB
low complexity region	879	898	N/A	INTRINSIC
SAM	914	980	1.6e-11	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000177992
AA Change: V11A

PolyPhen 2 Score 0.326 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000136820
Gene: ENSMUSG00000037652
AA Change: V11A

Domain	Start	End	E-Value	Type
low complexity region	6	28	N/A	INTRINSIC
low complexity region	60	77	N/A	INTRINSIC
low complexity region	80	130	N/A	INTRINSIC
low complexity region	140	154	N/A	INTRINSIC
low complexity region	288	314	N/A	INTRINSIC
low complexity region	348	374	N/A	INTRINSIC
low complexity region	467	493	N/A	INTRINSIC
low complexity region	519	533	N/A	INTRINSIC
low complexity region	538	568	N/A	INTRINSIC
low complexity region	607	615	N/A	INTRINSIC
low complexity region	625	653	N/A	INTRINSIC
PDB:2L8E\|A	742	778	8e-9	PDB
low complexity region	846	865	N/A	INTRINSIC
SAM	881	948	4.04e-13	SMART

Meta Mutation Damage Score

0.0724

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 95.1%

Validation Efficiency

97% (86/89)

Allele List at MGI

Other mutations in this stock

Total: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
6430548M08Rik	A	G	8: 120,886,756 (GRCm39)	N343D	probably damaging	Het
9530002B09Rik	T	A	4: 122,594,979 (GRCm39)	D78E	possibly damaging	Het
A2m	C	A	6: 121,634,365 (GRCm39)	D632E	probably benign	Het
Alpk2	A	G	18: 65,440,035 (GRCm39)	S453P	probably damaging	Het
Birc2	A	T	9: 7,833,675 (GRCm39)	F269I	probably damaging	Het
Ccdc66	G	A	14: 27,222,468 (GRCm39)	P92S	probably benign	Het
Cdc34	T	A	10: 79,523,869 (GRCm39)	D108E	possibly damaging	Het
Cdk5rap2	A	C	4: 70,184,997 (GRCm39)	V1151G	probably damaging	Het
Cemip	T	C	7: 83,607,747 (GRCm39)	K753R	probably damaging	Het
Cep295	A	T	9: 15,246,095 (GRCm39)	L787Q	possibly damaging	Het
Cideb	T	C	14: 55,995,727 (GRCm39)	N8S	probably benign	Het
Dagla	A	G	19: 10,248,373 (GRCm39)	Y96H	probably damaging	Het
Dapl1	C	A	2: 59,335,086 (GRCm39)	T80K	possibly damaging	Het
Ddx6	T	C	9: 44,535,784 (GRCm39)	V171A	probably damaging	Het
Dnah12	C	A	14: 26,494,551 (GRCm39)	T34K	probably damaging	Het
Dnhd1	T	C	7: 105,327,256 (GRCm39)	L735P	probably damaging	Het
Ep400	T	A	5: 110,881,763 (GRCm39)		probably benign	Het
Erlin1	G	T	19: 44,057,758 (GRCm39)	Y22*	probably null	Het
Gmcl1	A	G	6: 86,699,605 (GRCm39)	S141P	probably damaging	Het
Gtf2a1	C	T	12: 91,529,700 (GRCm39)	V338I	possibly damaging	Het
H2-T15	A	T	17: 36,368,559 (GRCm39)	M123K	probably damaging	Het
Ighv1-66	T	A	12: 115,557,016 (GRCm39)	Q22L	possibly damaging	Het
Igkv4-80	T	C	6: 68,993,720 (GRCm39)	Y57C	probably damaging	Het
Itpk1	G	A	12: 102,536,416 (GRCm39)	A410V	possibly damaging	Het
Itsn1	T	A	16: 91,617,471 (GRCm39)		probably benign	Het
Kcnk3	G	T	5: 30,745,730 (GRCm39)	A24S	probably damaging	Het
Kif20a	A	G	18: 34,765,664 (GRCm39)	Y887C	probably damaging	Het
Klf13	T	C	7: 63,587,718 (GRCm39)	T193A	possibly damaging	Het
Klhl9	G	T	4: 88,640,144 (GRCm39)	H32Q	probably damaging	Het
Kndc1	C	G	7: 139,481,159 (GRCm39)	P82A	probably damaging	Het
Llgl1	T	A	11: 60,602,908 (GRCm39)	L861Q	probably damaging	Het
Lpcat2	A	G	8: 93,615,999 (GRCm39)	E305G	probably damaging	Het
Mib2	C	A	4: 155,741,744 (GRCm39)	A293S	probably damaging	Het
Mtfr1	A	G	3: 19,269,766 (GRCm39)	E138G	probably damaging	Het
Myoz1	A	G	14: 20,700,663 (GRCm39)	W185R	probably damaging	Het
Ninj1	T	A	13: 49,347,442 (GRCm39)		probably null	Het
Nlgn2	A	T	11: 69,725,104 (GRCm39)	V54E	possibly damaging	Het
Nlrc5	A	C	8: 95,203,903 (GRCm39)	I668L	probably damaging	Het
Npy6r	T	A	18: 44,409,262 (GRCm39)	C228S	probably damaging	Het
Nufip2	T	C	11: 77,632,554 (GRCm39)	V690A	unknown	Het
Nup107	T	C	10: 117,602,273 (GRCm39)	I513M	probably benign	Het
Oit3	T	C	10: 59,261,284 (GRCm39)	D461G	probably damaging	Het
Or2ab1	T	A	11: 58,488,830 (GRCm39)	F205I	probably benign	Het
Paxbp1	T	C	16: 90,831,011 (GRCm39)	D455G	probably damaging	Het
Pcdh7	A	T	5: 57,878,625 (GRCm39)	T727S	probably damaging	Het
Pex14	G	A	4: 149,055,053 (GRCm39)	A113V	probably damaging	Het
Plec	T	C	15: 76,115,406 (GRCm39)	D56G	possibly damaging	Het
Plekha7	C	A	7: 115,836,768 (GRCm39)		probably benign	Het
Prdm16	T	C	4: 154,422,140 (GRCm39)	E885G	probably damaging	Het
Prss1l	T	C	6: 41,373,701 (GRCm39)	L188P	probably benign	Het
Psd2	A	G	18: 36,145,881 (GRCm39)	T762A	probably benign	Het
Psme4	T	A	11: 30,784,318 (GRCm39)	H964Q	probably damaging	Het
Rbak	C	T	5: 143,161,878 (GRCm39)	V51I	probably benign	Het
Rbfa	A	G	18: 80,243,721 (GRCm39)	L15P	probably benign	Het
Ren1	T	C	1: 133,282,546 (GRCm39)	Y84H	probably damaging	Het
Rps6ka5	A	T	12: 100,547,577 (GRCm39)	I311N	probably damaging	Het
Samd14	T	A	11: 94,912,361 (GRCm39)		probably null	Het
Scaf4	T	C	16: 90,026,403 (GRCm39)		probably benign	Het
Serpina12	A	T	12: 104,004,611 (GRCm39)	L7Q	unknown	Het
Serpinb9d	A	T	13: 33,384,599 (GRCm39)	E192V	probably damaging	Het
Slc22a29	A	T	19: 8,146,655 (GRCm39)	F382L	probably benign	Het
Snta1	T	A	2: 154,220,035 (GRCm39)	D375V	probably benign	Het
Stat5b	T	A	11: 100,678,064 (GRCm39)	Y683F	probably damaging	Het
Strip1	A	T	3: 107,531,819 (GRCm39)	Y257N	probably benign	Het
Sugp2	A	G	8: 70,704,548 (GRCm39)	H695R	probably benign	Het
Svep1	T	A	4: 58,068,526 (GRCm39)	R3087*	probably null	Het
Syngr2	T	C	11: 117,703,947 (GRCm39)	V138A	probably damaging	Het
Thra	T	C	11: 98,655,310 (GRCm39)	F397L	probably benign	Het
Tmem45b	T	A	9: 31,339,951 (GRCm39)	I149F	probably damaging	Het
Tmprss11f	C	T	5: 86,687,553 (GRCm39)		probably null	Het
Ush2a	C	T	1: 188,183,995 (GRCm39)	T1433I	probably benign	Het
Vmn2r109	A	T	17: 20,774,820 (GRCm39)	Y178*	probably null	Het
Vmn2r84	T	G	10: 130,226,582 (GRCm39)	M419L	probably benign	Het
Wnk2	C	T	13: 49,244,313 (GRCm39)	D508N	probably damaging	Het
Zfp268	T	A	4: 145,343,747 (GRCm39)		probably null	Het
Zfp276	A	G	8: 123,995,145 (GRCm39)		probably benign	Het
Zfp568	T	G	7: 29,697,617 (GRCm39)	F100V	probably benign	Het
Zfp667	T	A	7: 6,293,624 (GRCm39)	D41E	possibly damaging	Het

Other mutations in Phc3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00924:Phc3	APN	3	30,990,624 (GRCm39)	missense	probably damaging	0.98
IGL00985:Phc3	APN	3	30,968,346 (GRCm39)	missense	probably benign	0.13
IGL01340:Phc3	APN	3	30,984,033 (GRCm39)	missense	possibly damaging	0.85
IGL01450:Phc3	APN	3	30,968,653 (GRCm39)	missense	probably damaging	1.00
IGL01546:Phc3	APN	3	31,015,888 (GRCm39)	missense	probably damaging	1.00
IGL01918:Phc3	APN	3	30,968,565 (GRCm39)	critical splice donor site	probably null
IGL02178:Phc3	APN	3	30,984,012 (GRCm39)	missense	possibly damaging	0.47
IGL02210:Phc3	APN	3	30,990,858 (GRCm39)	missense	probably damaging	0.99
IGL02330:Phc3	APN	3	30,990,530 (GRCm39)	missense	probably damaging	1.00
IGL02516:Phc3	APN	3	31,002,942 (GRCm39)	missense	probably damaging	1.00
IGL03030:Phc3	APN	3	30,991,002 (GRCm39)	missense	probably damaging	1.00
See_saw	UTSW	3	30,991,198 (GRCm39)	nonsense	probably null
R1228:Phc3	UTSW	3	30,976,404 (GRCm39)	missense	possibly damaging	0.71
R1239:Phc3	UTSW	3	30,968,279 (GRCm39)	missense	probably damaging	1.00
R1319:Phc3	UTSW	3	30,984,018 (GRCm39)	missense	probably damaging	0.97
R1521:Phc3	UTSW	3	30,990,724 (GRCm39)	missense	possibly damaging	0.89
R1772:Phc3	UTSW	3	31,015,969 (GRCm39)	missense	probably damaging	1.00
R1793:Phc3	UTSW	3	31,002,865 (GRCm39)	missense	probably damaging	1.00
R1879:Phc3	UTSW	3	30,968,607 (GRCm39)	missense	probably damaging	1.00
R2171:Phc3	UTSW	3	31,005,078 (GRCm39)	missense	probably damaging	1.00
R2419:Phc3	UTSW	3	31,005,027 (GRCm39)	missense	probably damaging	0.99
R2863:Phc3	UTSW	3	30,968,277 (GRCm39)	missense	probably damaging	0.99
R2864:Phc3	UTSW	3	30,968,277 (GRCm39)	missense	probably damaging	0.99
R3700:Phc3	UTSW	3	30,968,277 (GRCm39)	missense	probably damaging	1.00
R3980:Phc3	UTSW	3	30,991,080 (GRCm39)	missense	probably damaging	0.99
R4222:Phc3	UTSW	3	30,990,968 (GRCm39)	missense	probably damaging	1.00
R4223:Phc3	UTSW	3	30,990,968 (GRCm39)	missense	probably damaging	1.00
R4928:Phc3	UTSW	3	31,005,068 (GRCm39)	missense	probably damaging	1.00
R5100:Phc3	UTSW	3	30,976,348 (GRCm39)	missense	possibly damaging	0.71
R5340:Phc3	UTSW	3	30,961,616 (GRCm39)	missense	probably damaging	1.00
R5656:Phc3	UTSW	3	31,020,015 (GRCm39)	missense	probably damaging	0.98
R5840:Phc3	UTSW	3	30,990,732 (GRCm39)	missense	possibly damaging	0.95
R6022:Phc3	UTSW	3	30,984,174 (GRCm39)	missense	probably damaging	1.00
R6061:Phc3	UTSW	3	30,968,678 (GRCm39)	missense	probably damaging	1.00
R6177:Phc3	UTSW	3	30,996,714 (GRCm39)	missense	probably damaging	1.00
R6188:Phc3	UTSW	3	30,991,198 (GRCm39)	nonsense	probably null
R6866:Phc3	UTSW	3	30,968,680 (GRCm39)	nonsense	probably null
R6870:Phc3	UTSW	3	30,990,910 (GRCm39)	missense	probably damaging	1.00
R7155:Phc3	UTSW	3	30,968,346 (GRCm39)	missense	probably benign	0.01
R7603:Phc3	UTSW	3	30,961,601 (GRCm39)	missense	probably damaging	0.97
R7874:Phc3	UTSW	3	30,990,863 (GRCm39)	missense	probably benign	0.00
R8422:Phc3	UTSW	3	30,984,039 (GRCm39)	nonsense	probably null
R8877:Phc3	UTSW	3	30,968,271 (GRCm39)	missense	probably damaging	1.00
R8972:Phc3	UTSW	3	31,015,926 (GRCm39)	missense	possibly damaging	0.95
R9003:Phc3	UTSW	3	31,020,007 (GRCm39)	missense	possibly damaging	0.86
R9042:Phc3	UTSW	3	30,983,916 (GRCm39)	missense	unknown
R9155:Phc3	UTSW	3	30,968,691 (GRCm39)	missense	probably benign	0.01
R9168:Phc3	UTSW	3	30,961,544 (GRCm39)	missense	probably benign
X0025:Phc3	UTSW	3	31,020,035 (GRCm39)	missense	probably damaging	0.96
Z1176:Phc3	UTSW	3	30,990,746 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- CAACACAGACAGCTGACGTG -3'
(R):5'- GGCCTTCCTAGAAATTTAGGCTC -3'

Sequencing Primer
(F):5'- CGTGGGCACAACAGTATGC -3'
(R):5'- AGAAATTTAGGCTCTTTCTTTTTCCC -3'

Posted On

2015-09-24