Mutagenetix > Incidental Mutation

Incidental Mutation 'R3829:Yrdc'

273882

Institutional Source

Beutler Lab

Gene Symbol

Yrdc

Ensembl Gene

ENSMUSG00000028889

Gene Name

yrdC domain containing (E.coli)

Synonyms

IRIP

MMRRC Submission

040776-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.962) question?

Stock #

R3829 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

124744552-124749035 bp(+) (GRCm39)

Type of Mutation

start codon destroyed

DNA Base Change (assembly)

T to A at 124745554 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 1 (M1K)

Ref Sequence

ENSEMBL: ENSMUSP00000114150 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030723] [ENSMUST00000064444] [ENSMUST00000102628] [ENSMUST00000106190] [ENSMUST00000106193] [ENSMUST00000137769] [ENSMUST00000144851] [ENSMUST00000185036] [ENSMUST00000163946]

AlphaFold

Q3U5F4

Predicted Effect

probably benign
Transcript: ENSMUST00000030723

SMART Domains

Protein: ENSMUSP00000030723
Gene: ENSMUSG00000028890

Domain	Start	End	E-Value	Type
ZnF_C2H2	139	163	1.22e-4	SMART
ZnF_C2H2	169	193	6.42e-4	SMART
ZnF_C2H2	199	223	2.4e-3	SMART
ZnF_C2H2	228	252	2.57e-3	SMART
ZnF_C2H2	258	282	2.57e-3	SMART
ZnF_C2H2	288	312	7.37e-4	SMART
low complexity region	429	456	N/A	INTRINSIC
low complexity region	500	526	N/A	INTRINSIC
low complexity region	545	558	N/A	INTRINSIC
low complexity region	628	638	N/A	INTRINSIC
low complexity region	656	669	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000064444

SMART Domains

Protein: ENSMUSP00000066000
Gene: ENSMUSG00000042763

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
low complexity region	31	46	N/A	INTRINSIC
low complexity region	55	79	N/A	INTRINSIC
Pfam:Glyco_hydro_99	95	445	8.7e-160	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000102628
AA Change: M154K

PolyPhen 2 Score 0.922 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000099688
Gene: ENSMUSG00000028889
AA Change: M154K

Domain	Start	End	E-Value	Type
low complexity region	32	63	N/A	INTRINSIC
Pfam:Sua5_yciO_yrdC	76	256	1.3e-46	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000106190

SMART Domains

Protein: ENSMUSP00000101796
Gene: ENSMUSG00000078570

Domain	Start	End	E-Value	Type
Pfam:DUF4726	10	110	2e-66	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000106193

SMART Domains

Protein: ENSMUSP00000101799
Gene: ENSMUSG00000028890

Domain	Start	End	E-Value	Type
ZnF_C2H2	139	163	1.22e-4	SMART
ZnF_C2H2	169	193	6.42e-4	SMART
ZnF_C2H2	199	223	2.4e-3	SMART
ZnF_C2H2	228	252	2.57e-3	SMART
ZnF_C2H2	258	282	2.57e-3	SMART
ZnF_C2H2	288	312	7.37e-4	SMART
low complexity region	429	456	N/A	INTRINSIC
low complexity region	500	526	N/A	INTRINSIC
low complexity region	545	558	N/A	INTRINSIC
low complexity region	628	638	N/A	INTRINSIC
low complexity region	656	669	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000125776

Predicted Effect

probably benign
Transcript: ENSMUST00000137769

Predicted Effect

probably null
Transcript: ENSMUST00000144851
AA Change: M1K

PolyPhen 2 Score 0.922 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000114150
Gene: ENSMUSG00000028889
AA Change: M1K

Domain	Start	End	E-Value	Type
Pfam:Sua5_yciO_yrdC	1	103	2.5e-20	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184704

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173434

Predicted Effect

probably benign
Transcript: ENSMUST00000185036

SMART Domains

Protein: ENSMUSP00000139121
Gene: ENSMUSG00000078570

Domain	Start	End	E-Value	Type
low complexity region	66	89	N/A	INTRINSIC
low complexity region	123	137	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000163946

Meta Mutation Damage Score

0.6151

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.7%
20x: 96.1%

Validation Efficiency

100% (54/54)

Allele List at MGI

Other mutations in this stock

Total: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4931414P19Rik	G	T	14: 54,821,966 (GRCm39)	H466Q	probably damaging	Het
4933411K16Rik	A	T	19: 42,041,322 (GRCm39)	H151L	probably damaging	Het
A330008L17Rik	A	G	8: 100,148,389 (GRCm39)		noncoding transcript	Het
Abcc5	C	A	16: 20,184,615 (GRCm39)	V1015L	probably benign	Het
Bach2	T	A	4: 32,563,150 (GRCm39)	L539H	probably damaging	Het
Birc6	A	G	17: 74,962,173 (GRCm39)	K3929R	probably damaging	Het
C1qtnf2	A	G	11: 43,382,148 (GRCm39)	D320G	probably benign	Het
Cbr2	A	T	11: 120,621,278 (GRCm39)	H140Q	probably benign	Het
Cbs	T	C	17: 31,836,355 (GRCm39)		probably benign	Het
Cdc42bpg	T	C	19: 6,367,675 (GRCm39)	V1015A	probably damaging	Het
Cep104	T	G	4: 154,069,400 (GRCm39)	M207R	probably damaging	Het
Chil6	A	T	3: 106,313,274 (GRCm39)	M25K	probably benign	Het
Cln5	A	G	14: 103,310,795 (GRCm39)	D154G	probably damaging	Het
Col4a1	C	A	8: 11,259,650 (GRCm39)	G1341V	probably damaging	Het
Commd9	C	A	2: 101,727,486 (GRCm39)	N93K	probably benign	Het
Cplane2	C	T	4: 140,945,900 (GRCm39)	R148C	probably damaging	Het
Cx3cl1	A	T	8: 95,503,934 (GRCm39)		probably benign	Het
Cyct	T	C	2: 76,184,512 (GRCm39)	K80E	probably damaging	Het
Dhx37	T	C	5: 125,508,677 (GRCm39)	K86R	probably benign	Het
Dnah17	G	A	11: 117,931,984 (GRCm39)		probably benign	Het
Etl4	T	C	2: 20,790,232 (GRCm39)	V628A	probably benign	Het
Fam234a	T	C	17: 26,437,163 (GRCm39)	E172G	probably benign	Het
Foxp2	C	T	6: 15,379,830 (GRCm39)		probably benign	Het
Frem1	A	T	4: 82,917,167 (GRCm39)	F592Y	probably damaging	Het
Gm10259	T	G	3: 25,266,693 (GRCm39)		noncoding transcript	Het
Gm17521	C	A	X: 121,938,922 (GRCm39)	G149C	unknown	Het
Gpat4	G	A	8: 23,670,171 (GRCm39)	P286L	probably damaging	Het
Grpel1	T	A	5: 36,626,827 (GRCm39)	N36K	probably benign	Het
Hap1	G	T	11: 100,246,847 (GRCm39)	D19E	probably damaging	Het
Lpcat1	T	C	13: 73,637,212 (GRCm39)	I114T	possibly damaging	Het
Mast4	G	T	13: 102,875,319 (GRCm39)	H1350N	probably damaging	Het
Mrpl50	T	C	4: 49,514,539 (GRCm39)	E44G	probably damaging	Het
Myg1	G	C	15: 102,246,171 (GRCm39)	G349R	probably damaging	Het
Myh1	A	G	11: 67,096,423 (GRCm39)	I301V	probably benign	Het
Ncapg2	A	T	12: 116,370,938 (GRCm39)		probably benign	Het
Ncor2	T	C	5: 125,195,756 (GRCm39)		probably benign	Het
Neo1	A	G	9: 58,820,452 (GRCm39)	Y824H	possibly damaging	Het
Or1o4	T	A	17: 37,591,140 (GRCm39)	Y57F	probably damaging	Het
Orc1	T	A	4: 108,462,828 (GRCm39)	M635K	probably damaging	Het
Phip	A	G	9: 82,753,698 (GRCm39)	I1682T	probably benign	Het
Ppp2r1b	A	G	9: 50,773,794 (GRCm39)	N223S	probably benign	Het
Ralb	A	T	1: 119,399,447 (GRCm39)	C204S	probably benign	Het
Rgs12	G	A	5: 35,123,359 (GRCm39)	V381M	possibly damaging	Het
Rtkn2	A	T	10: 67,833,456 (GRCm39)		probably null	Het
Srrm3	A	G	5: 135,886,068 (GRCm39)	D336G	probably damaging	Het
Stk11	T	C	10: 79,963,782 (GRCm39)		probably null	Het
Svep1	A	G	4: 58,096,177 (GRCm39)	L1481P	probably damaging	Het
Tiam2	C	G	17: 3,557,976 (GRCm39)		probably benign	Het
Tmem59l	A	G	8: 70,939,951 (GRCm39)	L6S	unknown	Het
Tmprss11b	T	C	5: 86,809,449 (GRCm39)	T348A	probably damaging	Het
Ube3b	C	A	5: 114,538,012 (GRCm39)	Q368K	probably damaging	Het
Veph1	T	A	3: 66,066,748 (GRCm39)	E413D	possibly damaging	Het
Vmn2r91	T	G	17: 18,325,759 (GRCm39)	W126G	probably damaging	Het
Zfp445	T	C	9: 122,682,142 (GRCm39)	M600V	probably benign	Het

Other mutations in Yrdc

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00157:Yrdc	APN	4	124,747,754 (GRCm39)	missense	probably damaging	1.00
IGL01142:Yrdc	APN	4	124,747,787 (GRCm39)	missense	probably damaging	0.98
R0525:Yrdc	UTSW	4	124,745,559 (GRCm39)	missense	probably damaging	1.00
R1162:Yrdc	UTSW	4	124,748,254 (GRCm39)	unclassified	probably benign
R1220:Yrdc	UTSW	4	124,748,329 (GRCm39)	missense	possibly damaging	0.62
R1952:Yrdc	UTSW	4	124,745,739 (GRCm39)	missense	probably benign	0.00
R7121:Yrdc	UTSW	4	124,744,748 (GRCm39)	missense	probably benign	0.06
R7272:Yrdc	UTSW	4	124,744,820 (GRCm39)	missense	probably benign	0.23
R8169:Yrdc	UTSW	4	124,744,880 (GRCm39)	missense	probably benign
R8837:Yrdc	UTSW	4	124,747,677 (GRCm39)	missense	probably benign	0.01
R9159:Yrdc	UTSW	4	124,747,811 (GRCm39)	critical splice donor site	probably null
Z1176:Yrdc	UTSW	4	124,745,290 (GRCm39)	unclassified	probably benign

Predicted Primers

PCR Primer
(F):5'- AGTCTGTCTTCTGCCAGAAC -3'
(R):5'- GAAGGCATGGTCAGGAATCC -3'

Sequencing Primer
(F):5'- GGTAGATCTCGTTCATTATACACGCG -3'
(R):5'- CATGGTCAGGAATCCGGATGC -3'

Posted On

2015-04-02