Mutagenetix > Incidental Mutation

Incidental Mutation 'R5304:Prdm13'

404410

Institutional Source

Beutler Lab

Gene Symbol

Prdm13

Ensembl Gene

ENSMUSG00000040478

Gene Name

PR domain containing 13

Synonyms

MMRRC Submission

042887-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5304 (G1)

Quality Score

159

Status

Validated

Chromosome

Chromosomal Location

21677480-21685963 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 21678984 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 502 (Y502C)

Ref Sequence

ENSEMBL: ENSMUSP00000092761 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000076206] [ENSMUST00000095141]

AlphaFold

E9PZZ1

Predicted Effect

probably benign
Transcript: ENSMUST00000076206
AA Change: Y454C

PolyPhen 2 Score 0.161 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000075562
Gene: ENSMUSG00000040478
AA Change: Y454C

Domain	Start	End	E-Value	Type
Blast:SET	2	118	4e-72	BLAST
PDB:3EP0\|B	56	132	1e-8	PDB
ZnF_C2H2	137	159	3.34e-2	SMART
low complexity region	204	220	N/A	INTRINSIC
low complexity region	231	252	N/A	INTRINSIC
low complexity region	267	275	N/A	INTRINSIC
low complexity region	302	335	N/A	INTRINSIC
low complexity region	336	350	N/A	INTRINSIC
low complexity region	353	370	N/A	INTRINSIC
low complexity region	392	404	N/A	INTRINSIC
low complexity region	546	571	N/A	INTRINSIC
ZnF_C2H2	572	594	4.4e-2	SMART
ZnF_C2H2	600	622	1.92e-2	SMART
ZnF_C2H2	629	652	2.79e-4	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000095141
AA Change: Y502C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000092761
Gene: ENSMUSG00000040478
AA Change: Y502C

Domain	Start	End	E-Value	Type
Blast:SET	42	166	1e-73	BLAST
PDB:3EP0\|B	104	180	1e-8	PDB
ZnF_C2H2	185	207	3.34e-2	SMART
low complexity region	252	268	N/A	INTRINSIC
low complexity region	279	300	N/A	INTRINSIC
low complexity region	315	323	N/A	INTRINSIC
low complexity region	350	383	N/A	INTRINSIC
low complexity region	384	398	N/A	INTRINSIC
low complexity region	401	418	N/A	INTRINSIC
low complexity region	440	452	N/A	INTRINSIC
low complexity region	594	619	N/A	INTRINSIC
ZnF_C2H2	620	642	4.4e-2	SMART
ZnF_C2H2	648	670	1.92e-2	SMART
ZnF_C2H2	677	700	2.79e-4	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139255

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139568

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144160

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149516

Meta Mutation Damage Score

0.2955

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.5%
20x: 95.9%

Validation Efficiency

99% (87/88)

MGI Phenotype

PHENOTYPE: Mice homozygous for a knock-out allele show a specific reduction in the number of GABAergic and glycinergic amacrine cells, a thin retinal inner nuclear layer, altered retinal inner plexiform layer morphology, and abnormally increased spatial, temporal, and contrast sensitivities in optokinetic reponses. [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
Adcy1	C	T	11: 7,014,198 (GRCm39)	A200V	probably benign	Het
Adgrv1	T	C	13: 81,726,372 (GRCm39)	D551G	possibly damaging	Het
Aldh3a2	A	G	11: 61,144,538 (GRCm39)	V340A	probably damaging	Het
Amy1	C	A	3: 113,352,013 (GRCm39)	C393F	probably damaging	Het
Ankrd16	T	C	2: 11,794,545 (GRCm39)	V310A	probably benign	Het
Arhgef15	T	C	11: 68,838,063 (GRCm39)	S686G	probably null	Het
Arid4b	T	A	13: 14,361,514 (GRCm39)	N659K	probably benign	Het
Asz1	C	T	6: 18,076,619 (GRCm39)	R191Q	probably benign	Het
Atp2a3	A	G	11: 72,879,383 (GRCm39)	I947V	probably damaging	Het
AW011738	G	A	4: 156,287,969 (GRCm39)		probably benign	Het
Bfsp1	G	T	2: 143,669,211 (GRCm39)	T456K	probably benign	Het
Cdc25c	T	C	18: 34,883,864 (GRCm39)	T40A	possibly damaging	Het
Cdh20	G	A	1: 110,036,569 (GRCm39)	C583Y	probably damaging	Het
Ceacam23	A	C	7: 17,636,617 (GRCm39)	E231D	probably benign	Het
Cfap54	A	T	10: 92,656,968 (GRCm39)	L3028Q	probably damaging	Het
Chd1	A	G	17: 15,975,213 (GRCm39)	S1088G	probably benign	Het
Chd1	A	T	17: 15,990,530 (GRCm39)	H1694L	possibly damaging	Het
Cstf3	G	T	2: 104,493,735 (GRCm39)	E580*	probably null	Het
Dip2a	A	T	10: 76,130,357 (GRCm39)	M622K	possibly damaging	Het
Dlgap1	A	T	17: 71,122,202 (GRCm39)	H877L	probably damaging	Het
Egfr	G	T	11: 16,834,260 (GRCm39)	M122I	probably benign	Het
Etfbkmt	T	A	6: 149,048,704 (GRCm39)	D114E	probably damaging	Het
Eva1c	T	C	16: 90,666,551 (GRCm39)	L158P	probably damaging	Het
Exo1	G	A	1: 175,720,542 (GRCm39)	V287M	probably damaging	Het
Fam171a1	T	C	2: 3,226,654 (GRCm39)	Y471H	probably damaging	Het
Fermt1	T	A	2: 132,783,986 (GRCm39)	T8S	probably benign	Het
Fgfr2	G	T	7: 129,769,504 (GRCm39)	P630T	probably damaging	Het
Fmo5	G	A	3: 97,558,938 (GRCm39)	G466E	probably damaging	Het
Hcn4	A	G	9: 58,751,215 (GRCm39)	I280M	probably benign	Het
Ifi208	A	C	1: 173,511,174 (GRCm39)	K443T	probably benign	Het
Irs3	A	G	5: 137,643,003 (GRCm39)	F145S	probably benign	Het
Kirrel1	T	A	3: 86,996,902 (GRCm39)	H300L	probably benign	Het
Krit1	A	G	5: 3,869,326 (GRCm39)	Q340R	probably damaging	Het
Lipo5	T	C	19: 33,445,149 (GRCm39)	D140G	unknown	Het
Lrrtm4	A	T	6: 79,999,683 (GRCm39)	Q365L	probably benign	Het
Lrwd1	G	T	5: 136,160,004 (GRCm39)	T353K	possibly damaging	Het
Lsm14a	A	T	7: 34,053,154 (GRCm39)	S240R	possibly damaging	Het
Map3k5	A	G	10: 19,983,984 (GRCm39)	I870V	probably benign	Het
Matcap2	A	T	9: 22,335,528 (GRCm39)	T49S	probably benign	Het
Mmp17	A	T	5: 129,671,678 (GRCm39)	E76V	probably null	Het
Mphosph10	A	G	7: 64,038,732 (GRCm39)	F272L	probably damaging	Het
Mtcl2	G	A	2: 156,865,737 (GRCm39)	Q1127*	probably null	Het
Myh10	A	G	11: 68,655,071 (GRCm39)	K380R	probably damaging	Het
Myo3b	C	T	2: 70,257,232 (GRCm39)	P1282L	probably damaging	Het
Nemp2	T	C	1: 52,682,238 (GRCm39)		probably benign	Het
Ola1	T	C	2: 73,029,778 (GRCm39)	I114V	probably damaging	Het
Or4c3d	T	A	2: 89,882,257 (GRCm39)	H137L	probably benign	Het
Or8k28	T	A	2: 86,285,779 (GRCm39)	T279S	probably damaging	Het
Pabpc4	T	G	4: 123,184,100 (GRCm39)	D204E	probably benign	Het
Pigr	A	T	1: 130,777,230 (GRCm39)	M679L	probably benign	Het
Pik3c2b	A	T	1: 132,998,146 (GRCm39)	M341L	possibly damaging	Het
Plin4	T	A	17: 56,413,132 (GRCm39)	T498S	probably benign	Het
Ppp2r5e	A	G	12: 75,562,459 (GRCm39)	S15P	possibly damaging	Het
Ptprk	T	C	10: 28,468,050 (GRCm39)		probably null	Het
Rapgef6	T	C	11: 54,548,200 (GRCm39)	S505P	probably benign	Het
Rgmb	G	T	17: 16,040,990 (GRCm39)	S199*	probably null	Het
Rgsl1	T	C	1: 153,703,238 (GRCm39)	T173A	probably damaging	Het
Rhobtb1	G	T	10: 69,105,742 (GRCm39)	K102N	probably damaging	Het
Ripor2	A	T	13: 24,858,649 (GRCm39)	D147V	probably damaging	Het
Rsad2	A	T	12: 26,500,681 (GRCm39)	V202E	probably damaging	Het
Slc1a6	A	G	10: 78,629,141 (GRCm39)	N186S	probably damaging	Het
Sorbs3	G	A	14: 70,422,345 (GRCm39)	R622*	probably null	Het
Spag9	C	A	11: 93,959,838 (GRCm39)	D342E	probably damaging	Het
Srgap3	T	C	6: 112,743,900 (GRCm39)	Y446C	probably damaging	Het
Thsd7b	C	T	1: 129,605,980 (GRCm39)	R574*	probably null	Het
Tmem74	A	T	15: 43,730,217 (GRCm39)	Y275*	probably null	Het
Topors	A	T	4: 40,262,541 (GRCm39)	S248T	possibly damaging	Het
Trpm1	A	T	7: 63,858,694 (GRCm39)	Y239F	probably benign	Het
Ttn	T	A	2: 76,548,527 (GRCm39)	Y30179F	possibly damaging	Het
Ugt2b34	A	T	5: 87,040,724 (GRCm39)	F399L	probably damaging	Het
Ush2a	A	T	1: 188,088,995 (GRCm39)	I317F	probably damaging	Het
Usp1	T	C	4: 98,822,855 (GRCm39)	V723A	probably benign	Het
Usp34	T	G	11: 23,293,616 (GRCm39)	L237V	probably damaging	Het
Vgf	A	T	5: 137,061,140 (GRCm39)	D434V	probably damaging	Het
Vmn1r179	A	G	7: 23,628,100 (GRCm39)	N97S	probably benign	Het
Vps13a	A	G	19: 16,687,751 (GRCm39)	L899P	possibly damaging	Het
Vps33b	A	T	7: 79,924,001 (GRCm39)	I41F	probably damaging	Het
Zap70	A	T	1: 36,817,299 (GRCm39)	H210L	probably damaging	Het
Zc3h8	T	C	2: 128,770,835 (GRCm39)	D300G	probably benign	Het
Zfp958	C	A	8: 4,676,196 (GRCm39)	H55N	possibly damaging	Het

Other mutations in Prdm13

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02940:Prdm13	APN	4	21,683,421 (GRCm39)	nonsense	probably null
IGL03211:Prdm13	APN	4	21,678,492 (GRCm39)	missense	probably damaging	1.00
R0363:Prdm13	UTSW	4	21,679,737 (GRCm39)	missense	unknown
R0512:Prdm13	UTSW	4	21,678,490 (GRCm39)	missense	probably damaging	1.00
R0726:Prdm13	UTSW	4	21,683,914 (GRCm39)	missense	unknown
R1056:Prdm13	UTSW	4	21,678,544 (GRCm39)	missense	probably damaging	1.00
R1433:Prdm13	UTSW	4	21,678,909 (GRCm39)	missense	probably damaging	1.00
R2005:Prdm13	UTSW	4	21,685,695 (GRCm39)	utr 5 prime	probably benign
R2292:Prdm13	UTSW	4	21,683,914 (GRCm39)	missense	unknown
R2382:Prdm13	UTSW	4	21,678,277 (GRCm39)	missense	possibly damaging	0.73
R3620:Prdm13	UTSW	4	21,683,532 (GRCm39)	missense	unknown
R4039:Prdm13	UTSW	4	21,685,774 (GRCm39)	utr 5 prime	probably benign
R4417:Prdm13	UTSW	4	21,678,756 (GRCm39)	missense	probably benign	0.39
R4453:Prdm13	UTSW	4	21,679,464 (GRCm39)	missense	unknown
R4850:Prdm13	UTSW	4	21,678,243 (GRCm39)	missense	possibly damaging	0.92
R4864:Prdm13	UTSW	4	21,685,543 (GRCm39)	missense	unknown
R4934:Prdm13	UTSW	4	21,678,223 (GRCm39)	utr 3 prime	probably benign
R5138:Prdm13	UTSW	4	21,679,507 (GRCm39)	missense	unknown
R5394:Prdm13	UTSW	4	21,679,455 (GRCm39)	missense	unknown
R5909:Prdm13	UTSW	4	21,683,894 (GRCm39)	missense	unknown
R5964:Prdm13	UTSW	4	21,683,852 (GRCm39)	nonsense	probably null
R6261:Prdm13	UTSW	4	21,678,366 (GRCm39)	missense	probably damaging	1.00
R7166:Prdm13	UTSW	4	21,683,528 (GRCm39)	missense	unknown
R7175:Prdm13	UTSW	4	21,679,473 (GRCm39)	missense	unknown
R7549:Prdm13	UTSW	4	21,679,072 (GRCm39)	missense	probably damaging	1.00
R7966:Prdm13	UTSW	4	21,679,932 (GRCm39)	missense	unknown
R8319:Prdm13	UTSW	4	21,679,327 (GRCm39)	missense	unknown
R8326:Prdm13	UTSW	4	21,679,557 (GRCm39)	missense	unknown
R8701:Prdm13	UTSW	4	21,678,615 (GRCm39)	missense	probably damaging	1.00
R8924:Prdm13	UTSW	4	21,679,125 (GRCm39)	missense	possibly damaging	0.94
R8947:Prdm13	UTSW	4	21,678,817 (GRCm39)	missense	probably damaging	1.00
R9165:Prdm13	UTSW	4	21,679,659 (GRCm39)	missense	unknown
R9168:Prdm13	UTSW	4	21,679,659 (GRCm39)	missense	unknown
R9170:Prdm13	UTSW	4	21,679,659 (GRCm39)	missense	unknown
R9171:Prdm13	UTSW	4	21,679,659 (GRCm39)	missense	unknown
Z1176:Prdm13	UTSW	4	21,679,518 (GRCm39)	missense	unknown
Z1177:Prdm13	UTSW	4	21,679,623 (GRCm39)	missense	unknown

Predicted Primers

PCR Primer
(F):5'- ATCTCGGACAGCTGCTGTG -3'
(R):5'- AGGCCTGCCATTCTACCCAG -3'

Sequencing Primer
(F):5'- ATCTCGCGGTCGATGCTG -3'
(R):5'- ACCATCCCAAGTGCCTGCTG -3'

Posted On

2016-07-22