Mutagenetix > Incidental Mutation

Incidental Mutation 'R7305:Prdm5'

567228

Institutional Source

Beutler Lab

Gene Symbol

Prdm5

Ensembl Gene

ENSMUSG00000029913

Gene Name

PR domain containing 5

Synonyms

6530401I24Rik, PFM2, E130112L17Rik, 4432417F03Rik

MMRRC Submission

045407-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7305 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

65755972-65913994 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 65808244 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Arginine at position 63 (S63R)

Ref Sequence

ENSEMBL: ENSMUSP00000031976 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000031973] [ENSMUST00000031976] [ENSMUST00000081219] [ENSMUST00000172638]

AlphaFold

Q9CXE0

Predicted Effect

possibly damaging
Transcript: ENSMUST00000031973
AA Change: S63R

PolyPhen 2 Score 0.954 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000031973
Gene: ENSMUSG00000029913
AA Change: S63R

Domain	Start	End	E-Value	Type
PDB:3EP0\|B	4	101	1e-11	PDB
Blast:SET	8	100	4e-64	BLAST
ZnF_C2H2	105	127	3.16e-3	SMART
ZnF_C2H2	133	155	8.81e-2	SMART
ZnF_C2H2	161	183	1.95e-3	SMART
ZnF_C2H2	189	211	6.78e-3	SMART
ZnF_C2H2	217	240	1.2e-3	SMART
ZnF_C2H2	246	268	4.87e-4	SMART
ZnF_C2H2	274	296	2.4e-3	SMART
ZnF_C2H2	302	324	2.43e-4	SMART
ZnF_C2H2	330	352	3.21e-4	SMART
ZnF_C2H2	358	380	1.45e-2	SMART
ZnF_C2H2	387	410	1.43e-1	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000031976
AA Change: S63R

PolyPhen 2 Score 0.827 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000031976
Gene: ENSMUSG00000029913
AA Change: S63R

Domain	Start	End	E-Value	Type
SET	8	130	2.01e-4	SMART
ZnF_C2H2	167	190	3.39e-3	SMART
ZnF_C2H2	199	221	1.04e-3	SMART
ZnF_C2H2	231	256	1.26e-2	SMART
ZnF_C2H2	264	286	1.95e-3	SMART
ZnF_C2H2	289	311	3.16e-3	SMART
ZnF_C2H2	317	339	8.81e-2	SMART
ZnF_C2H2	345	367	1.95e-3	SMART
ZnF_C2H2	373	395	6.78e-3	SMART
ZnF_C2H2	401	424	1.2e-3	SMART
ZnF_C2H2	430	452	4.87e-4	SMART
ZnF_C2H2	458	480	2.4e-3	SMART
ZnF_C2H2	486	508	2.43e-4	SMART
ZnF_C2H2	514	536	3.21e-4	SMART
ZnF_C2H2	542	564	1.45e-2	SMART
ZnF_C2H2	571	594	1.43e-1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000081219
AA Change: S35R

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000079979
Gene: ENSMUSG00000029913
AA Change: S35R

Domain	Start	End	E-Value	Type
Blast:SET	8	72	2e-34	BLAST
ZnF_C2H2	80	102	2.4e-3	SMART
ZnF_C2H2	108	130	2.43e-4	SMART
ZnF_C2H2	136	158	3.21e-4	SMART
ZnF_C2H2	164	186	1.45e-2	SMART
ZnF_C2H2	193	216	1.43e-1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000172638
AA Change: S63R

PolyPhen 2 Score 0.246 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000133423
Gene: ENSMUSG00000029913
AA Change: S63R

Domain	Start	End	E-Value	Type
SET	8	130	2.01e-4	SMART
ZnF_C2H2	167	190	3.39e-3	SMART
ZnF_C2H2	199	221	1.04e-3	SMART
ZnF_C2H2	231	256	1.26e-2	SMART
ZnF_C2H2	264	286	1.95e-3	SMART
ZnF_C2H2	289	311	3.16e-3	SMART
ZnF_C2H2	317	339	8.81e-2	SMART
ZnF_C2H2	345	367	1.95e-3	SMART
ZnF_C2H2	373	395	6.78e-3	SMART
ZnF_C2H2	401	424	1.2e-3	SMART
ZnF_C2H2	430	452	4.87e-4	SMART
ZnF_C2H2	458	480	2.4e-3	SMART

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a transcription factor of the PR-domain protein family. It contains a PR-domain and multiple zinc finger motifs. Transcription factors of the PR-domain family are known to be involved in cell differentiation and tumorigenesis. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a hypomorphic allele display delayed bone ossification with reduced collagen fibril formation, total bone area, bone mineral content and bone mineral density. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abhd16b	A	T	2: 181,135,209 (GRCm39)	D37V	possibly damaging	Het
Ankhd1	A	G	18: 36,765,258 (GRCm39)	D87G		Het
Ankrd31	A	G	13: 97,015,479 (GRCm39)	S1583G	probably damaging	Het
Ankub1	T	C	3: 57,599,938 (GRCm39)		probably benign	Het
Apba3	A	G	10: 81,107,067 (GRCm39)	D264G	probably damaging	Het
Armh3	A	T	19: 45,880,560 (GRCm39)	M508K	probably benign	Het
Asap1	G	A	15: 64,002,099 (GRCm39)	T404M	probably damaging	Het
Cnot3	A	T	7: 3,648,479 (GRCm39)		probably benign	Het
Cxxc1	A	G	18: 74,352,467 (GRCm39)	Y349C	probably benign	Het
Cyfip1	AGTGT	AGT	7: 55,577,937 (GRCm39)		probably null	Het
Cyp3a57	A	G	5: 145,307,795 (GRCm39)	I184V	probably benign	Het
D130052B06Rik	GTCTACACTGTCCTGCACAGGTGACCCATCTACCCCGTCCTATCCTGGCGACCCATCTACACTGTCCTG	GTCTACACTGTCCTG	11: 33,573,355 (GRCm39)		probably null	Het
Dab1	T	A	4: 104,570,987 (GRCm39)	D210E		Het
Elavl1	G	A	8: 4,375,199 (GRCm39)		probably benign	Het
Emilin1	C	T	5: 31,074,433 (GRCm39)	Q225*	probably null	Het
Eml6	G	T	11: 29,727,258 (GRCm39)	A1288E	probably benign	Het
Eno1	T	C	4: 150,329,796 (GRCm39)		probably null	Het
Eprs1	C	T	1: 185,111,898 (GRCm39)	R303C	probably damaging	Het
Eps15l1	G	A	8: 73,126,878 (GRCm39)	A651V	probably benign	Het
Etl4	A	T	2: 20,714,368 (GRCm39)	I156F	probably damaging	Het
Faim2	A	T	15: 99,411,814 (GRCm39)	I171N	probably damaging	Het
Fam135a	T	A	1: 24,069,939 (GRCm39)	N381I	probably damaging	Het
Fhip1a	G	T	3: 85,637,831 (GRCm39)	P156Q	probably damaging	Het
Gabrg3	T	A	7: 56,384,833 (GRCm39)	M243L	probably benign	Het
Garin2	A	G	12: 78,761,809 (GRCm39)	K158E	possibly damaging	Het
Gm5134	A	G	10: 75,836,233 (GRCm39)	I405V	probably damaging	Het
Gm9376	A	T	14: 118,504,768 (GRCm39)	K67*	probably null	Het
Grm8	A	T	6: 27,761,354 (GRCm39)	I290K	possibly damaging	Het
Hao1	T	A	2: 134,390,121 (GRCm39)	M73L	probably benign	Het
Herc1	A	G	9: 66,369,150 (GRCm39)	D452G		Het
Idh3b	C	A	2: 130,123,413 (GRCm39)	K192N	possibly damaging	Het
Igkv6-23	A	G	6: 70,237,553 (GRCm39)	S63P	probably benign	Het
Itgb2	A	C	10: 77,384,398 (GRCm39)	D173A	probably damaging	Het
Jmjd8	A	T	17: 26,049,301 (GRCm39)	T255S	probably benign	Het
Lamc3	A	C	2: 31,820,714 (GRCm39)	E1243A	probably benign	Het
Map1a	A	G	2: 121,129,939 (GRCm39)	T252A	probably damaging	Het
Mrgpra1	C	A	7: 46,985,203 (GRCm39)	A159S	probably benign	Het
Ndst3	T	C	3: 123,395,131 (GRCm39)	I500V	possibly damaging	Het
Nhsl1	A	G	10: 18,407,434 (GRCm39)	T1523A	possibly damaging	Het
Nr2f1	A	G	13: 78,343,298 (GRCm39)	I322T	probably damaging	Het
Nup210	T	C	6: 91,064,948 (GRCm39)	E184G	probably damaging	Het
Obsl1	C	T	1: 75,470,590 (GRCm39)	W1022*	probably null	Het
Or2l13	T	A	16: 19,306,449 (GRCm39)	I287N	probably damaging	Het
Or4a77	T	A	2: 89,486,846 (GRCm39)	H313L	probably benign	Het
Or52p2	G	T	7: 102,237,162 (GRCm39)	Q263K	possibly damaging	Het
Or5p51	A	T	7: 107,444,572 (GRCm39)	Y123N	probably damaging	Het
Or6c1	A	T	10: 129,518,149 (GRCm39)	I153N	probably damaging	Het
Or6c65	T	A	10: 129,603,720 (GRCm39)	Y118*	probably null	Het
Otulinl	A	G	15: 27,658,319 (GRCm39)	C184R	probably benign	Het
Oxr1	C	T	15: 41,677,004 (GRCm39)	P187L	not run	Het
Parp8	A	G	13: 117,031,461 (GRCm39)	L417P	possibly damaging	Het
Pdia6	A	G	12: 17,324,509 (GRCm39)	Q120R	probably benign	Het
Ppp3cc	T	C	14: 70,478,252 (GRCm39)	N290S	probably benign	Het
Prr14l	T	C	5: 32,988,445 (GRCm39)	D350G	probably benign	Het
Pwwp2a	T	C	11: 43,607,878 (GRCm39)	L497S	probably damaging	Het
R3hdm2	A	G	10: 127,312,547 (GRCm39)	N430D	probably benign	Het
Rad51ap2	A	G	12: 11,507,344 (GRCm39)	N422S	possibly damaging	Het
Rbbp8	G	A	18: 11,805,638 (GRCm39)		probably null	Het
Rsf1	GGCGGCGGC	GGCGGCGGCAGCGGCGGC	7: 97,229,125 (GRCm39)		probably benign	Het
Slc22a6	G	A	19: 8,599,522 (GRCm39)		probably null	Het
Slc28a3	T	A	13: 58,714,045 (GRCm39)	E440V	possibly damaging	Het
Slc30a5	A	T	13: 100,947,932 (GRCm39)	I482K	probably damaging	Het
Slco1a1	A	T	6: 141,870,223 (GRCm39)	F305Y	probably damaging	Het
Slco1a8	G	A	6: 141,938,220 (GRCm39)	A253V	probably damaging	Het
Slco4c1	T	C	1: 96,756,690 (GRCm39)	N544S	probably damaging	Het
Smpd4	T	A	16: 17,459,647 (GRCm39)	I656N	probably damaging	Het
Spata31h1	A	T	10: 82,120,953 (GRCm39)	I4019K	probably benign	Het
Taok1	A	T	11: 77,432,500 (GRCm39)	L771*	probably null	Het
Tmem231	T	C	8: 112,641,927 (GRCm39)	D209G	possibly damaging	Het
Tmem25	A	G	9: 44,706,705 (GRCm39)		probably null	Het
Tmem79	T	C	3: 88,240,718 (GRCm39)	T77A	probably benign	Het
Topbp1	A	T	9: 103,205,836 (GRCm39)	T825S	probably damaging	Het
Trpm6	A	T	19: 18,853,455 (GRCm39)	Q1825L	probably benign	Het
Uba1y	T	A	Y: 821,348 (GRCm39)	D110E	probably damaging	Het
Utrn	A	T	10: 12,261,280 (GRCm39)	N3422K	probably benign	Het
Vmn1r219	A	T	13: 23,347,314 (GRCm39)	M168L	probably benign	Het
Vmn2r62	T	C	7: 42,414,235 (GRCm39)	H736R	possibly damaging	Het
Wdr1	T	C	5: 38,697,435 (GRCm39)	H291R	possibly damaging	Het
Zan	T	C	5: 137,413,401 (GRCm39)	T3177A	unknown	Het
Zbtb21	T	C	16: 97,752,495 (GRCm39)	H596R	possibly damaging	Het

Other mutations in Prdm5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01395:Prdm5	APN	6	65,847,374 (GRCm39)	missense	possibly damaging	0.93
IGL02363:Prdm5	APN	6	65,771,303 (GRCm39)	missense	probably damaging	1.00
IGL02457:Prdm5	APN	6	65,858,100 (GRCm39)	missense	probably damaging	1.00
IGL03190:Prdm5	APN	6	65,833,116 (GRCm39)	splice site	probably benign
IGL03239:Prdm5	APN	6	65,863,062 (GRCm39)	splice site	probably benign
IGL03377:Prdm5	APN	6	65,836,457 (GRCm39)	missense	possibly damaging	0.93
R0329:Prdm5	UTSW	6	65,839,887 (GRCm39)	splice site	probably benign
R0926:Prdm5	UTSW	6	65,860,531 (GRCm39)	missense	probably damaging	0.99
R1458:Prdm5	UTSW	6	65,860,585 (GRCm39)	missense	probably damaging	0.99
R1859:Prdm5	UTSW	6	65,808,263 (GRCm39)	missense	probably benign	0.03
R1956:Prdm5	UTSW	6	65,913,060 (GRCm39)	missense	probably damaging	1.00
R1996:Prdm5	UTSW	6	65,913,072 (GRCm39)	missense	probably damaging	1.00
R1997:Prdm5	UTSW	6	65,913,072 (GRCm39)	missense	probably damaging	1.00
R2019:Prdm5	UTSW	6	65,808,340 (GRCm39)	missense	probably damaging	0.99
R3082:Prdm5	UTSW	6	65,913,069 (GRCm39)	missense	probably damaging	1.00
R3819:Prdm5	UTSW	6	65,913,041 (GRCm39)	missense	possibly damaging	0.92
R4411:Prdm5	UTSW	6	65,878,771 (GRCm39)	nonsense	probably null
R4981:Prdm5	UTSW	6	65,847,446 (GRCm39)	missense	probably damaging	0.99
R5077:Prdm5	UTSW	6	65,756,158 (GRCm39)	missense	probably damaging	0.97
R5089:Prdm5	UTSW	6	65,833,074 (GRCm39)	missense	probably benign	0.01
R5138:Prdm5	UTSW	6	65,833,086 (GRCm39)	nonsense	probably null
R5735:Prdm5	UTSW	6	65,904,974 (GRCm39)	missense	possibly damaging	0.93
R6355:Prdm5	UTSW	6	65,860,578 (GRCm39)	missense	probably damaging	1.00
R6743:Prdm5	UTSW	6	65,860,635 (GRCm39)	missense	probably damaging	1.00
R6769:Prdm5	UTSW	6	65,839,920 (GRCm39)	missense	probably damaging	0.98
R7216:Prdm5	UTSW	6	65,904,967 (GRCm39)	nonsense	probably null
R7510:Prdm5	UTSW	6	65,904,976 (GRCm39)	missense	probably damaging	0.97
R8270:Prdm5	UTSW	6	65,913,058 (GRCm39)	missense	probably damaging	1.00
R8529:Prdm5	UTSW	6	65,878,829 (GRCm39)	missense	probably damaging	1.00
R8856:Prdm5	UTSW	6	65,860,569 (GRCm39)	missense	possibly damaging	0.80
R9283:Prdm5	UTSW	6	65,858,060 (GRCm39)	missense	probably damaging	0.98
R9427:Prdm5	UTSW	6	65,771,321 (GRCm39)	missense	possibly damaging	0.65
R9477:Prdm5	UTSW	6	65,771,342 (GRCm39)	missense	possibly damaging	0.48
X0017:Prdm5	UTSW	6	65,846,246 (GRCm39)	missense	possibly damaging	0.94

Predicted Primers

PCR Primer
(F):5'- GGCTTCTGTAGACATAAGTTTAAGCC -3'
(R):5'- CCTGCATATGCCGACTACATG -3'

Sequencing Primer
(F):5'- GACATAAGTTTAAGCCATGAGTGTTG -3'
(R):5'- GCATATGCCGACTACATGATTTC -3'

Posted On

2019-06-26