Mutagenetix > Incidental Mutation

Incidental Mutation 'R8701:Prdm13'

669046

Institutional Source

Beutler Lab

Gene Symbol

Prdm13

Ensembl Gene

ENSMUSG00000040478

Gene Name

PR domain containing 13

Synonyms

MMRRC Submission

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R8701 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

21677480-21685963 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 21678615 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Tyrosine at position 625 (C625Y)

Ref Sequence

ENSEMBL: ENSMUSP00000092761 (fasta)

Gene Model

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

AlphaFold

E9PZZ1

Predicted Effect

probably damaging
Transcript: ENSMUST00000076206
AA Change: C577Y

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

SMART Domains

Protein: ENSMUSP00000075562
Gene: ENSMUSG00000040478
AA Change: C577Y

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: C625Y

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

SMART Domains

Protein: ENSMUSP00000092761
Gene: ENSMUSG00000040478
AA Change: C625Y

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.8%

Validation Efficiency

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: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4931408C20Rik	A	T	1: 26,685,445	V218D	probably benign	Het
Abcc4	T	C	14: 118,599,373	I659V	probably benign	Het
Adamtsl4	T	A	3: 95,684,966	D24V	possibly damaging	Het
Agtr1b	A	T	3: 20,316,092	F117I	probably damaging	Het
Aldh3b2	A	G	19: 3,978,448	E116G	probably damaging	Het
Alox5	T	A	6: 116,413,826	I455F	possibly damaging	Het
Arnt	C	T	3: 95,493,765	S675F	possibly damaging	Het
C330027C09Rik	T	A	16: 49,007,141	Y456*	probably null	Het
Camkv	A	G	9: 107,948,041	T414A	possibly damaging	Het
Cd209c	C	T	8: 3,945,892	R6H	probably benign	Het
Cnr1	A	G	4: 33,944,739	I376V	probably benign	Het
Cyp2j12	T	A	4: 96,121,573	K183M	possibly damaging	Het
Dact3	G	T	7: 16,885,276	R232L	probably damaging	Het
Dlg5	G	A	14: 24,176,700	T378M	probably benign	Het
Dnah10	T	A	5: 124,726,847	D79E	probably benign	Het
Dsc1	A	T	18: 20,107,682	Y195*	probably null	Het
Elovl1	A	T	4: 118,430,510	M1L	probably benign	Het
Fam107a	A	G	14: 8,298,755	F124L	probably damaging	Het
Fam219a	A	G	4: 41,520,283	M155T	probably damaging	Het
Gm28308	C	G	6: 52,163,450		probably benign	Het
Gpr153	C	T	4: 152,279,101		probably benign	Het
Gtf2ird2	T	A	5: 134,216,235	I445N	probably damaging	Het
Gzmb	A	T	14: 56,260,360	V141E	probably benign	Het
Hmcn1	A	T	1: 150,755,257	M930K	probably benign	Het
Hunk	T	A	16: 90,386,610	F52Y	probably damaging	Het
Il18rap	A	G	1: 40,539,341	E304G	probably benign	Het
Klk14	A	G	7: 43,694,142	S133G	possibly damaging	Het
Man2b1	T	C	8: 85,095,153	S695P	probably damaging	Het
Mccc1	A	T	3: 35,995,784	D86E	probably benign	Het
Mcu	T	A	10: 59,467,653	I121F	probably damaging	Het
Mlxipl	T	C	5: 135,107,191	F90S	possibly damaging	Het
Muc2	A	G	7: 141,695,607	D536G	probably damaging	Het
Naa11	T	C	5: 97,391,958	S114G	possibly damaging	Het
Ncaph	T	C	2: 127,106,138	K676E	probably benign	Het
Neurl2	C	T	2: 164,833,134	D103N	probably benign	Het
Nup210l	T	C	3: 90,122,814	M278T	probably benign	Het
Olfr1192-ps1	A	G	2: 88,652,487	I112V	possibly damaging	Het
Olfr550	A	T	7: 102,578,692	M66L	possibly damaging	Het
Olfr897-ps1	A	T	9: 38,309,438	L214F	unknown	Het
Olfr967	A	T	9: 39,750,914	H176L	probably damaging	Het
Olfr981	A	G	9: 40,022,519	N42S	probably damaging	Het
Pcdh20	A	T	14: 88,468,413	Y484N	possibly damaging	Het
Pkhd1l1	A	G	15: 44,574,683	Y3598C	probably damaging	Het
Plcg2	T	A	8: 117,581,677	L336Q	probably damaging	Het
Ppp1r8	T	C	4: 132,830,642	D207G	possibly damaging	Het
Ptcd3	T	C	6: 71,885,511	D480G	possibly damaging	Het
Rbm39	T	A	2: 156,161,587	K291M	probably damaging	Het
Repin1	G	T	6: 48,597,345	E403*	probably null	Het
Rnf220	T	C	4: 117,489,993	H74R	probably damaging	Het
Sp6	A	T	11: 97,022,264	T268S	probably damaging	Het
Sphk2	A	T	7: 45,710,825	V585E	probably damaging	Het
Syne1	G	A	10: 5,205,026	Q5638*	probably null	Het
Tas1r3	C	T	4: 155,861,046	V573I	probably benign	Het
Tdrd1	T	C	19: 56,851,484	S659P	possibly damaging	Het
Tead4	T	A	6: 128,242,566	K237N	probably damaging	Het
Tex24	T	A	8: 27,345,124	C227S	probably benign	Het
Tom1	A	T	8: 75,052,168	T174S	probably benign	Het
Tpm3	C	T	3: 90,087,680	R168C	possibly damaging	Het
Trpv3	A	G	11: 73,278,936	E111G	possibly damaging	Het
Unc80	A	G	1: 66,638,032	D2040G	possibly damaging	Het
Usp47	A	G	7: 112,093,195	T955A	probably damaging	Het
Vmn2r11	G	A	5: 109,047,690	A590V	probably damaging	Het
Wisp2	G	T	2: 163,828,866	G98W	probably damaging	Het
Zfp112	A	G	7: 24,125,740	R382G	probably damaging	Het
Zfp606	T	A	7: 12,481,098	D84E	unknown	Het

Other mutations in Prdm13

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02940:Prdm13	APN	4	21683421	nonsense	probably null
IGL03211:Prdm13	APN	4	21678492	missense	probably damaging	1.00
R0363:Prdm13	UTSW	4	21679737	missense	unknown
R0512:Prdm13	UTSW	4	21678490	missense	probably damaging	1.00
R0726:Prdm13	UTSW	4	21683914	missense	unknown
R1056:Prdm13	UTSW	4	21678544	missense	probably damaging	1.00
R1433:Prdm13	UTSW	4	21678909	missense	probably damaging	1.00
R2005:Prdm13	UTSW	4	21685695	utr 5 prime	probably benign
R2292:Prdm13	UTSW	4	21683914	missense	unknown
R2382:Prdm13	UTSW	4	21678277	missense	possibly damaging	0.73
R3620:Prdm13	UTSW	4	21683532	missense	unknown
R4039:Prdm13	UTSW	4	21685774	utr 5 prime	probably benign
R4417:Prdm13	UTSW	4	21678756	missense	probably benign	0.39
R4453:Prdm13	UTSW	4	21679464	missense	unknown
R4850:Prdm13	UTSW	4	21678243	missense	possibly damaging	0.92
R4864:Prdm13	UTSW	4	21685543	missense	unknown
R4934:Prdm13	UTSW	4	21678223	utr 3 prime	probably benign
R5138:Prdm13	UTSW	4	21679507	missense	unknown
R5304:Prdm13	UTSW	4	21678984	missense	probably damaging	1.00
R5394:Prdm13	UTSW	4	21679455	missense	unknown
R5909:Prdm13	UTSW	4	21683894	missense	unknown
R5964:Prdm13	UTSW	4	21683852	nonsense	probably null
R6261:Prdm13	UTSW	4	21678366	missense	probably damaging	1.00
R7166:Prdm13	UTSW	4	21683528	missense	unknown
R7175:Prdm13	UTSW	4	21679473	missense	unknown
R7549:Prdm13	UTSW	4	21679072	missense	probably damaging	1.00
R7966:Prdm13	UTSW	4	21679932	missense	unknown
R8319:Prdm13	UTSW	4	21679327	missense	unknown
R8326:Prdm13	UTSW	4	21679557	missense	unknown
R8924:Prdm13	UTSW	4	21679125	missense	possibly damaging	0.94
R8947:Prdm13	UTSW	4	21678817	missense	probably damaging	1.00
R9165:Prdm13	UTSW	4	21679659	missense	unknown
R9168:Prdm13	UTSW	4	21679659	missense	unknown
R9170:Prdm13	UTSW	4	21679659	missense	unknown
R9171:Prdm13	UTSW	4	21679659	missense	unknown
Z1176:Prdm13	UTSW	4	21679518	missense	unknown
Z1177:Prdm13	UTSW	4	21679623	missense	unknown

Predicted Primers

PCR Primer
(F):5'- GACATCCACATCACTGTCCTCG -3'
(R):5'- ATCTCCTATCTGAGTGGCCC -3'

Sequencing Primer
(F):5'- ACTTGACGTGACGCTCCAG -3'
(R):5'- TCCCTGGCCAGCATCGAC -3'

Posted On

2021-04-30