Mutagenetix > Incidental Mutation

Incidental Mutation 'R7383:Phc1'

572867

Institutional Source

Beutler Lab

Gene Symbol

Phc1

Ensembl Gene

ENSMUSG00000040669

Gene Name

polyhomeotic 1

Synonyms

rae28, Mph1, Rae-28, Edr1

MMRRC Submission

045465-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7383 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

122294690-122317520 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 122300317 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 521 (S521P)

Ref Sequence

ENSEMBL: ENSMUSP00000078514 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000079560] [ENSMUST00000081849] [ENSMUST00000112600] [ENSMUST00000159252] [ENSMUST00000160163] [ENSMUST00000160696] [ENSMUST00000160843] [ENSMUST00000161054] [ENSMUST00000161739]

AlphaFold

no structure available at present

Predicted Effect

unknown
Transcript: ENSMUST00000079560
AA Change: S521P

SMART Domains

Protein: ENSMUSP00000078514
Gene: ENSMUSG00000040669
AA Change: S521P

Domain	Start	End	E-Value	Type
low complexity region	3	22	N/A	INTRINSIC
low complexity region	34	46	N/A	INTRINSIC
low complexity region	83	102	N/A	INTRINSIC
low complexity region	182	196	N/A	INTRINSIC
low complexity region	240	303	N/A	INTRINSIC
low complexity region	330	341	N/A	INTRINSIC
low complexity region	373	416	N/A	INTRINSIC
coiled coil region	420	446	N/A	INTRINSIC
low complexity region	448	480	N/A	INTRINSIC
low complexity region	485	506	N/A	INTRINSIC
low complexity region	524	535	N/A	INTRINSIC
low complexity region	543	556	N/A	INTRINSIC
low complexity region	575	587	N/A	INTRINSIC
low complexity region	617	628	N/A	INTRINSIC
low complexity region	704	722	N/A	INTRINSIC
Pfam:zf-FCS	798	833	4.9e-8	PFAM
low complexity region	855	869	N/A	INTRINSIC
SAM	943	1010	9.57e-15	SMART

Predicted Effect

unknown
Transcript: ENSMUST00000081849
AA Change: S469P

SMART Domains

Protein: ENSMUSP00000080532
Gene: ENSMUSG00000040669
AA Change: S469P

Domain	Start	End	E-Value	Type
low complexity region	3	22	N/A	INTRINSIC
low complexity region	34	46	N/A	INTRINSIC
low complexity region	83	102	N/A	INTRINSIC
low complexity region	188	251	N/A	INTRINSIC
low complexity region	278	289	N/A	INTRINSIC
low complexity region	321	364	N/A	INTRINSIC
coiled coil region	368	394	N/A	INTRINSIC
low complexity region	396	428	N/A	INTRINSIC
low complexity region	433	454	N/A	INTRINSIC
low complexity region	472	483	N/A	INTRINSIC
low complexity region	491	504	N/A	INTRINSIC
low complexity region	523	535	N/A	INTRINSIC
low complexity region	565	576	N/A	INTRINSIC
low complexity region	652	670	N/A	INTRINSIC
Pfam:zf-FCS	746	781	4.6e-8	PFAM
low complexity region	803	817	N/A	INTRINSIC
SAM	891	958	9.57e-15	SMART

Predicted Effect

unknown
Transcript: ENSMUST00000112600
AA Change: S469P

SMART Domains

Protein: ENSMUSP00000108219
Gene: ENSMUSG00000040669
AA Change: S469P

Domain	Start	End	E-Value	Type
low complexity region	3	22	N/A	INTRINSIC
low complexity region	34	46	N/A	INTRINSIC
low complexity region	83	102	N/A	INTRINSIC
low complexity region	188	251	N/A	INTRINSIC
low complexity region	278	289	N/A	INTRINSIC
low complexity region	321	364	N/A	INTRINSIC
coiled coil region	368	394	N/A	INTRINSIC
low complexity region	396	428	N/A	INTRINSIC
low complexity region	433	454	N/A	INTRINSIC
low complexity region	472	483	N/A	INTRINSIC
low complexity region	491	504	N/A	INTRINSIC
low complexity region	523	535	N/A	INTRINSIC
low complexity region	565	576	N/A	INTRINSIC
low complexity region	652	670	N/A	INTRINSIC
Pfam:zf-FCS	746	781	4.6e-8	PFAM
low complexity region	803	817	N/A	INTRINSIC
SAM	891	958	9.57e-15	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000159252
AA Change: S476P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000124678
Gene: ENSMUSG00000040669
AA Change: S476P

Domain	Start	End	E-Value	Type
low complexity region	3	22	N/A	INTRINSIC
low complexity region	46	65	N/A	INTRINSIC
low complexity region	137	151	N/A	INTRINSIC
low complexity region	195	258	N/A	INTRINSIC
low complexity region	285	296	N/A	INTRINSIC
low complexity region	328	371	N/A	INTRINSIC
coiled coil region	375	401	N/A	INTRINSIC
low complexity region	403	435	N/A	INTRINSIC
low complexity region	440	461	N/A	INTRINSIC
low complexity region	479	490	N/A	INTRINSIC
low complexity region	498	511	N/A	INTRINSIC
low complexity region	530	542	N/A	INTRINSIC
low complexity region	572	583	N/A	INTRINSIC
low complexity region	659	677	N/A	INTRINSIC
Pfam:zf-FCS	753	788	2.2e-8	PFAM
low complexity region	810	824	N/A	INTRINSIC
SAM	898	965	9.57e-15	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000160163

SMART Domains

Protein: ENSMUSP00000125545
Gene: ENSMUSG00000040669

Domain	Start	End	E-Value	Type
low complexity region	3	22	N/A	INTRINSIC
low complexity region	34	46	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000160696
AA Change: S521P

SMART Domains

Protein: ENSMUSP00000125580
Gene: ENSMUSG00000040669
AA Change: S521P

Domain	Start	End	E-Value	Type
low complexity region	3	22	N/A	INTRINSIC
low complexity region	34	46	N/A	INTRINSIC
low complexity region	83	102	N/A	INTRINSIC
low complexity region	182	196	N/A	INTRINSIC
low complexity region	240	303	N/A	INTRINSIC
low complexity region	330	341	N/A	INTRINSIC
low complexity region	373	416	N/A	INTRINSIC
coiled coil region	420	446	N/A	INTRINSIC
low complexity region	448	480	N/A	INTRINSIC
low complexity region	485	506	N/A	INTRINSIC
low complexity region	524	535	N/A	INTRINSIC
low complexity region	543	556	N/A	INTRINSIC
low complexity region	575	587	N/A	INTRINSIC
low complexity region	617	628	N/A	INTRINSIC
low complexity region	704	722	N/A	INTRINSIC
Pfam:PHC2_SAM_assoc	834	941	3.4e-31	PFAM
SAM	943	1010	9.57e-15	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000160843

SMART Domains

Protein: ENSMUSP00000125030
Gene: ENSMUSG00000040669

Domain	Start	End	E-Value	Type
low complexity region	3	22	N/A	INTRINSIC
low complexity region	34	46	N/A	INTRINSIC
low complexity region	83	102	N/A	INTRINSIC
low complexity region	182	196	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000161054
AA Change: S469P

SMART Domains

Protein: ENSMUSP00000123911
Gene: ENSMUSG00000040669
AA Change: S469P

Domain	Start	End	E-Value	Type
low complexity region	3	22	N/A	INTRINSIC
low complexity region	34	46	N/A	INTRINSIC
low complexity region	83	102	N/A	INTRINSIC
low complexity region	188	251	N/A	INTRINSIC
low complexity region	278	289	N/A	INTRINSIC
low complexity region	321	364	N/A	INTRINSIC
coiled coil region	368	394	N/A	INTRINSIC
low complexity region	396	428	N/A	INTRINSIC
low complexity region	433	454	N/A	INTRINSIC
low complexity region	472	483	N/A	INTRINSIC
low complexity region	491	504	N/A	INTRINSIC
low complexity region	523	535	N/A	INTRINSIC
low complexity region	565	576	N/A	INTRINSIC
low complexity region	652	670	N/A	INTRINSIC
Pfam:zf-FCS	746	781	4.6e-8	PFAM
low complexity region	803	817	N/A	INTRINSIC
SAM	891	958	9.57e-15	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000161290

SMART Domains

Protein: ENSMUSP00000125110
Gene: ENSMUSG00000040669

Domain	Start	End	E-Value	Type
low complexity region	17	29	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000161739
AA Change: S521P

SMART Domains

Protein: ENSMUSP00000125568
Gene: ENSMUSG00000040669
AA Change: S521P

Domain	Start	End	E-Value	Type
low complexity region	3	22	N/A	INTRINSIC
low complexity region	34	46	N/A	INTRINSIC
low complexity region	83	102	N/A	INTRINSIC
low complexity region	182	196	N/A	INTRINSIC
low complexity region	240	303	N/A	INTRINSIC
low complexity region	330	341	N/A	INTRINSIC
low complexity region	373	416	N/A	INTRINSIC
coiled coil region	420	446	N/A	INTRINSIC
low complexity region	448	480	N/A	INTRINSIC
low complexity region	485	506	N/A	INTRINSIC
low complexity region	524	535	N/A	INTRINSIC
low complexity region	543	556	N/A	INTRINSIC
low complexity region	575	587	N/A	INTRINSIC
low complexity region	617	628	N/A	INTRINSIC
low complexity region	704	722	N/A	INTRINSIC
Pfam:zf-FCS	798	833	4.9e-8	PFAM
low complexity region	855	869	N/A	INTRINSIC
SAM	943	1010	9.57e-15	SMART

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a homolog of the Drosophila polyhomeotic gene, which is a member of the Polycomb group of genes. The gene product is a component of a multimeric protein complex that contains EDR2 and the vertebrate Polycomb protein BMH1. The gene product, the EDR2 protein, and the Drosophila polyhomeotic protein share 2 highly conserved domains, named homology domains I and II. These domains are involved in protein-protein interactions and may mediate heterodimerization of the protein encoded by this gene and the EDR2 protein. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutant mice exhibit perinatal lethality, posterior skeletal transformations and defects in neural crest derived tissues, including ocular abnormalities, cleft palate, parathyroid and thymic hypoplasia and cardiac anomalies. Hematopoiesis is impaired in fetal livers. [provided by MGI curators]

Allele List at MGI

All alleles(147) : Targeted, knock-out(1) Gene trapped(146)

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aebp1	T	A	11: 5,818,548 (GRCm39)	I511N	probably damaging	Het
Ap5m1	T	G	14: 49,311,653 (GRCm39)	V241G	possibly damaging	Het
BC049715	T	A	6: 136,817,453 (GRCm39)	I231N	probably damaging	Het
Bckdhb	T	G	9: 83,835,766 (GRCm39)	V90G	possibly damaging	Het
Cep20	TTGTG	TTG	16: 14,118,009 (GRCm39)		probably null	Het
Chd8	T	C	14: 52,452,776 (GRCm39)	I1248V	probably damaging	Het
Ckap2l	A	T	2: 129,111,172 (GRCm39)	M675K	possibly damaging	Het
Ckap4	A	T	10: 84,364,148 (GRCm39)	V305E	probably damaging	Het
Clasrp	C	A	7: 19,319,198 (GRCm39)	R489L	unknown	Het
Col24a1	A	G	3: 145,004,599 (GRCm39)	I26V	probably benign	Het
Cort	C	T	4: 149,209,861 (GRCm39)	A64T	possibly damaging	Het
Dmkn	T	A	7: 30,464,793 (GRCm39)	N255K	unknown	Het
Dph2	A	T	4: 117,748,566 (GRCm39)	L69Q	probably damaging	Het
Fbxo11	A	G	17: 88,310,282 (GRCm39)	I432T		Het
Fgd3	T	C	13: 49,421,785 (GRCm39)	K531R	possibly damaging	Het
Fgd5	A	G	6: 91,964,099 (GRCm39)	K111E	probably benign	Het
Gdf6	T	A	4: 9,859,537 (GRCm39)	D206E	probably benign	Het
Gtpbp1	T	A	15: 79,600,354 (GRCm39)	L429Q	probably damaging	Het
Hk2	A	G	6: 82,726,276 (GRCm39)	F90S	probably damaging	Het
Hrnr	A	T	3: 93,239,098 (GRCm39)	Q3112L	unknown	Het
Hsd17b4	A	C	18: 50,297,917 (GRCm39)	K402T	probably benign	Het
Htr1f	T	C	16: 64,747,206 (GRCm39)	T29A	probably benign	Het
Ikbkb	C	A	8: 23,159,066 (GRCm39)	A471S	probably benign	Het
Inpp5f	A	G	7: 128,296,310 (GRCm39)	D887G	probably damaging	Het
Ipo9	A	G	1: 135,316,411 (GRCm39)	L805P	probably damaging	Het
Jmjd1c	A	T	10: 67,025,537 (GRCm39)	N118I	probably benign	Het
Kif26b	T	G	1: 178,358,275 (GRCm39)	C129G	probably damaging	Het
Mga	G	A	2: 119,790,821 (GRCm39)	A2236T	probably damaging	Het
Micu2	T	C	14: 58,154,810 (GRCm39)	Q405R	possibly damaging	Het
Myo1e	T	A	9: 70,204,577 (GRCm39)	V59D	probably damaging	Het
Nav3	A	G	10: 109,552,532 (GRCm39)	I1770T	probably damaging	Het
Ndufa10	A	T	1: 92,392,183 (GRCm39)	I190N	probably damaging	Het
Niban3	A	C	8: 72,056,470 (GRCm39)	E390A	possibly damaging	Het
Npat	T	A	9: 53,474,078 (GRCm39)	H623Q	probably benign	Het
Npc1l1	T	C	11: 6,167,777 (GRCm39)	T1005A	probably benign	Het
Or10ag58	A	G	2: 87,265,721 (GRCm39)	S297G	possibly damaging	Het
Or14c39	A	T	7: 86,343,960 (GRCm39)	I99F	probably damaging	Het
Or1e22	A	G	11: 73,376,715 (GRCm39)	*312Q	probably null	Het
Or2b4	A	G	17: 38,116,972 (GRCm39)	K312R	probably benign	Het
Or2w3	T	C	11: 58,557,011 (GRCm39)	S209P	possibly damaging	Het
Or5t7	A	G	2: 86,507,263 (GRCm39)	V138A	possibly damaging	Het
Or8s8	C	G	15: 98,354,578 (GRCm39)	P129R	probably damaging	Het
Pafah1b2	C	T	9: 45,880,147 (GRCm39)	G177R	probably benign	Het
Plpp2	A	T	10: 79,366,841 (GRCm39)	L25Q	probably null	Het
Plxna4	A	G	6: 32,129,734 (GRCm39)		probably null	Het
Ppl	G	T	16: 4,915,835 (GRCm39)	P576Q	probably damaging	Het
Rab38	T	C	7: 88,079,637 (GRCm39)	Y10H	possibly damaging	Het
Rbfox1	G	A	16: 6,887,899 (GRCm39)	G13S	probably benign	Het
Rhot1	C	G	11: 80,114,760 (GRCm39)	P56R	probably damaging	Het
Sipa1l2	A	G	8: 126,174,385 (GRCm39)	W1298R	probably damaging	Het
Slc16a14	G	A	1: 84,890,292 (GRCm39)	H338Y	probably damaging	Het
Slc8a3	T	G	12: 81,362,579 (GRCm39)	Y80S	probably damaging	Het
Slco6c1	A	T	1: 97,003,608 (GRCm39)	Y513*	probably null	Het
Smarcd2	A	G	11: 106,155,602 (GRCm39)	C405R	probably damaging	Het
Szt2	G	A	4: 118,222,411 (GRCm39)	R3198*	probably null	Het
Tmeff1	T	A	4: 48,636,841 (GRCm39)	C180S	probably damaging	Het
Tmem132a	A	T	19: 10,844,358 (GRCm39)	M80K	probably benign	Het
Tnfsf12	A	G	11: 69,577,892 (GRCm39)	V175A	probably damaging	Het
Tnpo2	G	A	8: 85,776,748 (GRCm39)	R485H	probably damaging	Het
Togaram2	A	T	17: 72,007,512 (GRCm39)	I354F	probably damaging	Het
Uchl5	T	A	1: 143,659,753 (GRCm39)	S42R	probably benign	Het
Virma	C	A	4: 11,514,026 (GRCm39)	L627I	probably damaging	Het
Vmn2r12	A	T	5: 109,240,684 (GRCm39)	I143K	probably benign	Het
Vmn2r95	T	G	17: 18,660,734 (GRCm39)	V382G	probably benign	Het
Wipf3	G	T	6: 54,462,263 (GRCm39)	A158S	probably benign	Het
Ylpm1	T	G	12: 85,091,242 (GRCm39)	S1809A	possibly damaging	Het
Zdhhc5	A	T	2: 84,524,748 (GRCm39)	C191S	probably benign	Het
Zer1	G	A	2: 30,001,253 (GRCm39)	R84C	probably damaging	Het
Zfhx2	A	T	14: 55,305,710 (GRCm39)	V991D	probably benign	Het
Zscan4b	C	A	7: 10,637,960 (GRCm39)	M61I	possibly damaging	Het
Zswim2	A	T	2: 83,745,672 (GRCm39)	S589T	possibly damaging	Het

Other mutations in Phc1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00340:Phc1	APN	6	122,299,958 (GRCm39)	splice site	probably benign
IGL01354:Phc1	APN	6	122,311,042 (GRCm39)	missense	probably damaging	1.00
IGL01786:Phc1	APN	6	122,296,479 (GRCm39)	missense	possibly damaging	0.82
IGL02110:Phc1	APN	6	122,298,994 (GRCm39)	missense	possibly damaging	0.91
IGL02479:Phc1	APN	6	122,300,676 (GRCm39)	unclassified	probably benign
IGL02861:Phc1	APN	6	122,300,748 (GRCm39)	unclassified	probably benign
IGL03106:Phc1	APN	6	122,300,428 (GRCm39)	unclassified	probably benign
3-1:Phc1	UTSW	6	122,315,423 (GRCm39)	intron	probably benign
FR4737:Phc1	UTSW	6	122,300,557 (GRCm39)	small insertion	probably benign
FR4976:Phc1	UTSW	6	122,300,559 (GRCm39)	small insertion	probably benign
R0452:Phc1	UTSW	6	122,299,995 (GRCm39)	missense	probably damaging	1.00
R1146:Phc1	UTSW	6	122,300,416 (GRCm39)	unclassified	probably benign
R1146:Phc1	UTSW	6	122,300,416 (GRCm39)	unclassified	probably benign
R1301:Phc1	UTSW	6	122,302,833 (GRCm39)	missense	probably benign	0.03
R1738:Phc1	UTSW	6	122,295,525 (GRCm39)	missense	probably damaging	1.00
R2056:Phc1	UTSW	6	122,310,299 (GRCm39)	missense	probably damaging	0.99
R2164:Phc1	UTSW	6	122,299,296 (GRCm39)	missense	possibly damaging	0.82
R2183:Phc1	UTSW	6	122,300,284 (GRCm39)	missense	probably damaging	1.00
R2424:Phc1	UTSW	6	122,297,002 (GRCm39)	missense	probably damaging	0.98
R4378:Phc1	UTSW	6	122,311,966 (GRCm39)	missense	possibly damaging	0.66
R4648:Phc1	UTSW	6	122,298,872 (GRCm39)	missense	possibly damaging	0.95
R4831:Phc1	UTSW	6	122,313,964 (GRCm39)	start gained	probably benign
R5244:Phc1	UTSW	6	122,298,938 (GRCm39)	missense	probably damaging	1.00
R5475:Phc1	UTSW	6	122,311,051 (GRCm39)	missense	possibly damaging	0.95
R6491:Phc1	UTSW	6	122,311,923 (GRCm39)
R6701:Phc1	UTSW	6	122,302,733 (GRCm39)	missense	probably damaging	0.96
R6733:Phc1	UTSW	6	122,313,845 (GRCm39)	missense	possibly damaging	0.77
R7022:Phc1	UTSW	6	122,311,990 (GRCm39)	missense	probably damaging	0.98
R7707:Phc1	UTSW	6	122,300,739 (GRCm39)	missense	unknown
R7825:Phc1	UTSW	6	122,299,340 (GRCm39)	missense	probably benign	0.26
R7846:Phc1	UTSW	6	122,310,329 (GRCm39)	missense	probably damaging	1.00
R8314:Phc1	UTSW	6	122,297,937 (GRCm39)	missense	unknown
R8346:Phc1	UTSW	6	122,302,774 (GRCm39)	missense	probably damaging	0.98
R8534:Phc1	UTSW	6	122,315,539 (GRCm39)	intron	probably benign
RF036:Phc1	UTSW	6	122,300,539 (GRCm39)	small insertion	probably benign
RF041:Phc1	UTSW	6	122,300,559 (GRCm39)	small insertion	probably benign
RF044:Phc1	UTSW	6	122,300,559 (GRCm39)	small insertion	probably benign
RF064:Phc1	UTSW	6	122,300,539 (GRCm39)	small insertion	probably benign
X0024:Phc1	UTSW	6	122,300,588 (GRCm39)	small deletion	probably benign
X0026:Phc1	UTSW	6	122,296,497 (GRCm39)	missense	possibly damaging	0.66

Predicted Primers

PCR Primer
(F):5'- TTCTTGAAGTGCACCAGGAGC -3'
(R):5'- AGCAGCAGATTGCCATCCAC -3'

Sequencing Primer
(F):5'- AGCCGCCTGTGATGAAGGTG -3'
(R):5'- GTCCCAGCTGCTTCACACAG -3'

Posted On

2019-09-13