Mutagenetix > Incidental Mutation

Incidental Mutation 'R2164:Phc1'

235345

Institutional Source

Beutler Lab

Gene Symbol

Phc1

Ensembl Gene

ENSMUSG00000040669

Gene Name

polyhomeotic 1

Synonyms

rae28, Rae-28, Mph1, Edr1

MMRRC Submission

040167-MU

Accession Numbers

Genbank: NM_007905, NM_001042623; MGI: 103248

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2164 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

122317731-122340561 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 122322337 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Aspartic acid at position 638 (N638D)

Ref Sequence

ENSEMBL: ENSMUSP00000124678 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000007602] [ENSMUST00000079560] [ENSMUST00000081849] [ENSMUST00000112600] [ENSMUST00000112610] [ENSMUST00000159252] [ENSMUST00000160163] [ENSMUST00000160696] [ENSMUST00000160843] [ENSMUST00000161054] [ENSMUST00000161739]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000007602

SMART Domains

Protein: ENSMUSP00000007602
Gene: ENSMUSG00000007458

Domain	Start	End	E-Value	Type
Pfam:Man-6-P_recep	1	278	4.5e-184	PFAM

Predicted Effect

unknown
Transcript: ENSMUST00000079560
AA Change: N683D

SMART Domains

Protein: ENSMUSP00000078514
Gene: ENSMUSG00000040669
AA Change: N683D

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: N631D

SMART Domains

Protein: ENSMUSP00000080532
Gene: ENSMUSG00000040669
AA Change: N631D

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: N631D

SMART Domains

Protein: ENSMUSP00000108219
Gene: ENSMUSG00000040669
AA Change: N631D

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: ENSMUST00000112610

SMART Domains

Protein: ENSMUSP00000108229
Gene: ENSMUSG00000007458

Domain	Start	End	E-Value	Type
Pfam:Man-6-P_recep	1	278	3.9e-200	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000159252
AA Change: N638D

PolyPhen 2 Score 0.820 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000124678
Gene: ENSMUSG00000040669
AA Change: N638D

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: N683D

SMART Domains

Protein: ENSMUSP00000125580
Gene: ENSMUSG00000040669
AA Change: N683D

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: N631D

SMART Domains

Protein: ENSMUSP00000123911
Gene: ENSMUSG00000040669
AA Change: N631D

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: N683D

SMART Domains

Protein: ENSMUSP00000125568
Gene: ENSMUSG00000040669
AA Change: N683D

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

noncoding transcript
Transcript: ENSMUST00000161877

SMART Domains

Protein: ENSMUSP00000123854
Gene: ENSMUSG00000040669

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

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.5%
20x: 95.6%

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: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca6	CTGTAGGAAATCTTCAATGT	CTGT	11: 110,210,193		probably null	Het
Adcy8	C	T	15: 64,920,934	G58S	probably benign	Het
Adgra2	T	A	8: 27,114,204	L24*	probably null	Het
Ampd2	C	A	3: 108,085,369		probably benign	Het
Ankrd26	T	G	6: 118,525,791	E806A	probably damaging	Het
Apol9b	A	G	15: 77,735,439	D145G	probably benign	Het
Ash1l	T	A	3: 88,985,419	M1535K	probably benign	Het
Atf6	A	G	1: 170,794,735	M439T	probably damaging	Het
B3glct	A	T	5: 149,754,156	M417L	probably damaging	Het
Cep192	A	T	18: 67,820,360	T483S	probably damaging	Het
Cep290	G	A	10: 100,518,795	E914K	probably damaging	Het
Chst15	C	T	7: 132,270,385	A56T	probably damaging	Het
Col27a1	A	T	4: 63,225,424	T450S	probably benign	Het
Cpsf2	A	G	12: 101,985,335	N177S	probably damaging	Het
Csmd3	CCTTTGCGCTT	CCTT	15: 47,741,236		probably null	Het
Ctc1	C	T	11: 69,035,615	A859V	possibly damaging	Het
Dcakd	A	G	11: 102,997,357	Y134H	possibly damaging	Het
Dctn3	G	T	4: 41,723,065	Y22*	probably null	Het
Dync2h1	T	A	9: 7,124,797	D2025V	probably damaging	Het
Dync2li1	T	C	17: 84,636,274	S92P	probably damaging	Het
Eml5	A	G	12: 98,887,097	V81A	probably damaging	Het
Espl1	C	T	15: 102,319,588	R1625C	probably damaging	Het
Fam181a	T	C	12: 103,316,526	V230A	probably benign	Het
Fam213b	T	G	4: 154,898,149	Y56S	probably damaging	Het
Fanci	T	A	7: 79,395,995	D28E	probably benign	Het
Fmn1	A	G	2: 113,365,617	N554S	unknown	Het
Frem2	T	C	3: 53,537,330	Y2460C	probably damaging	Het
Fscb	G	A	12: 64,473,793	P300S	probably damaging	Het
Gm28042	A	G	2: 120,036,748	D438G	probably benign	Het
Map1b	C	T	13: 99,429,338	V2292M	unknown	Het
Nbas	A	G	12: 13,330,646	D635G	possibly damaging	Het
Ncapg2	A	G	12: 116,450,475		probably null	Het
Nrp2	A	T	1: 62,744,355	E205V	probably damaging	Het
Pcdhb3	A	T	18: 37,302,186	T402S	possibly damaging	Het
Plcb1	A	G	2: 135,346,330	N781S	possibly damaging	Het
Prkdc	T	A	16: 15,705,207	D1164E	probably damaging	Het
Proser2	T	A	2: 6,100,695	R353W	possibly damaging	Het
Ptges	T	A	2: 30,892,696	T115S	probably benign	Het
Ptprk	A	T	10: 28,560,142	D833V	probably damaging	Het
Pum1	T	A	4: 130,728,083	L173*	probably null	Het
Pum1	G	T	4: 130,728,084	L269F	probably damaging	Het
Rasgrp4	A	G	7: 29,139,045	Y106C	probably damaging	Het
Rbbp6	T	A	7: 122,999,474		probably benign	Het
Rdh1	A	G	10: 127,760,172	T79A	possibly damaging	Het
Relb	A	C	7: 19,613,761		probably null	Het
Rnf122	G	A	8: 31,112,164	W6*	probably null	Het
Rnf31	A	G	14: 55,592,537	E138G	possibly damaging	Het
Scaf8	G	A	17: 3,197,210	R936Q	probably damaging	Het
Scube3	T	A	17: 28,166,134	V686D	possibly damaging	Het
Snrnp27	A	T	6: 86,676,214	C141S	probably benign	Het
Spns2	C	T	11: 72,458,671	V252M	possibly damaging	Het
Tmem159	A	G	7: 120,120,239	E157G	possibly damaging	Het
Tomm40l	C	T	1: 171,220,134	S220N	probably damaging	Het
Trim17	A	G	11: 58,971,411	D423G	probably damaging	Het
Trpc6	A	AT	9: 8,610,465		probably null	Het
Uba5	A	T	9: 104,060,243	M89K	probably damaging	Het
Vav2	T	C	2: 27,273,706	D628G	probably damaging	Het
Vmn2r107	T	C	17: 20,375,642	L819P	probably damaging	Het
Vmn2r25	A	T	6: 123,839,559	D354E	possibly damaging	Het
Xrn1	A	G	9: 96,006,820	E984G	possibly damaging	Het
Zbtb17	T	C	4: 141,464,246	V223A	probably benign	Het
Zcchc11	G	A	4: 108,503,029	R481Q	possibly damaging	Het
Zfp592	T	C	7: 81,041,438	S1122P	possibly damaging	Het

Other mutations in Phc1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00340:Phc1	APN	6	122322999	splice site	probably benign
IGL01354:Phc1	APN	6	122334083	missense	probably damaging	1.00
IGL01786:Phc1	APN	6	122319520	missense	possibly damaging	0.82
IGL02110:Phc1	APN	6	122322035	missense	possibly damaging	0.91
IGL02479:Phc1	APN	6	122323717	unclassified	probably benign
IGL02861:Phc1	APN	6	122323789	unclassified	probably benign
IGL03106:Phc1	APN	6	122323469	unclassified	probably benign
3-1:Phc1	UTSW	6	122338464	intron	probably benign
FR4737:Phc1	UTSW	6	122323598	small insertion	probably benign
FR4976:Phc1	UTSW	6	122323600	small insertion	probably benign
R0452:Phc1	UTSW	6	122323036	missense	probably damaging	1.00
R1146:Phc1	UTSW	6	122323457	unclassified	probably benign
R1146:Phc1	UTSW	6	122323457	unclassified	probably benign
R1301:Phc1	UTSW	6	122325874	missense	probably benign	0.03
R1738:Phc1	UTSW	6	122318566	missense	probably damaging	1.00
R2056:Phc1	UTSW	6	122333340	missense	probably damaging	0.99
R2183:Phc1	UTSW	6	122323325	missense	probably damaging	1.00
R2424:Phc1	UTSW	6	122320043	missense	probably damaging	0.98
R4378:Phc1	UTSW	6	122335007	missense	possibly damaging	0.66
R4648:Phc1	UTSW	6	122321913	missense	possibly damaging	0.95
R4831:Phc1	UTSW	6	122337005	start gained	probably benign
R5244:Phc1	UTSW	6	122321979	missense	probably damaging	1.00
R5475:Phc1	UTSW	6	122334092	missense	possibly damaging	0.95
R6491:Phc1	UTSW	6	122334964
R6701:Phc1	UTSW	6	122325774	missense	probably damaging	0.96
R6733:Phc1	UTSW	6	122336886	missense	possibly damaging	0.77
R7022:Phc1	UTSW	6	122335031	missense	probably damaging	0.98
R7383:Phc1	UTSW	6	122323358	missense	unknown
R7707:Phc1	UTSW	6	122323780	missense	unknown
R7825:Phc1	UTSW	6	122322381	missense	probably benign	0.26
R7846:Phc1	UTSW	6	122333370	missense	probably damaging	1.00
R8314:Phc1	UTSW	6	122320978	missense	unknown
R8346:Phc1	UTSW	6	122325815	missense	probably damaging	0.98
R8534:Phc1	UTSW	6	122338580	intron	probably benign
RF036:Phc1	UTSW	6	122323580	small insertion	probably benign
RF041:Phc1	UTSW	6	122323600	small insertion	probably benign
RF044:Phc1	UTSW	6	122323600	small insertion	probably benign
RF064:Phc1	UTSW	6	122323580	small insertion	probably benign
X0024:Phc1	UTSW	6	122323629	small deletion	probably benign
X0026:Phc1	UTSW	6	122319538	missense	possibly damaging	0.66

Predicted Primers

PCR Primer
(F):5'- TGTAGATGACACAACTGACCCG -3'
(R):5'- CACACCTAAATCATAGCTGCTTTC -3'

Sequencing Primer
(F):5'- GCCCATTACCAAGCCTGATC -3'
(R):5'- GCTTTCTTGTTTATTCCTCTCTAGGG -3'

Posted On

2014-10-01