Mutagenetix > Incidental Mutation

Incidental Mutation 'R8169:Yrdc'

643794

Institutional Source

Beutler Lab

Gene Symbol

Yrdc

Ensembl Gene

ENSMUSG00000028889

Gene Name

yrdC domain containing (E.coli)

Synonyms

IRIP

MMRRC Submission

067595-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.962) question?

Stock #

R8169 (G1)

Quality Score

68.0074

Status

Validated

Chromosome

Chromosomal Location

124744552-124749035 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 124744880 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Glycine at position 105 (S105G)

Ref Sequence

ENSEMBL: ENSMUSP00000099688 (fasta)

Gene Model

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

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

probably benign
Transcript: ENSMUST00000102628
AA Change: S105G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000099688
Gene: ENSMUSG00000028889
AA Change: S105G

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 benign
Transcript: ENSMUST00000144851

SMART Domains

Protein: ENSMUSP00000114150
Gene: ENSMUSG00000028889

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

Predicted Effect

probably benign
Transcript: ENSMUST00000163946

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

Meta Mutation Damage Score

0.0846

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

99% (80/81)

Allele List at MGI

Other mutations in this stock

Total: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3110082I17Rik	C	A	5: 139,349,812 (GRCm39)	G79V	probably damaging	Het
4930562C15Rik	T	A	16: 4,684,082 (GRCm39)	Y226N	probably benign	Het
Arhgap45	G	A	10: 79,863,706 (GRCm39)	A819T	probably damaging	Het
Bach1	G	A	16: 87,519,390 (GRCm39)	C560Y	possibly damaging	Het
Capn13	T	A	17: 73,633,467 (GRCm39)		probably null	Het
Casq2	G	T	3: 102,017,628 (GRCm39)	A103S	possibly damaging	Het
Cfap100	A	G	6: 90,394,656 (GRCm39)	F57S		Het
Clca3a2	A	T	3: 144,783,653 (GRCm39)	L654Q	probably damaging	Het
Cntnap5c	T	A	17: 58,411,765 (GRCm39)		probably null	Het
Cplane2	A	G	4: 140,945,530 (GRCm39)	H127R	probably damaging	Het
Crtc2	G	C	3: 90,170,883 (GRCm39)	G652A	probably damaging	Het
Csnk1g2	A	G	10: 80,475,636 (GRCm39)	D401G	probably damaging	Het
Dars1	T	C	1: 128,304,002 (GRCm39)	N242D	probably null	Het
Dnah10	T	C	5: 124,877,946 (GRCm39)	L2677P	probably damaging	Het
Dnal1	G	A	12: 84,171,330 (GRCm39)	A3T	probably benign	Het
Dpep2	C	T	8: 106,722,849 (GRCm39)	V60I		Het
Eeig1	T	C	2: 32,453,760 (GRCm39)	I203T	probably benign	Het
Ehmt2	T	A	17: 35,122,339 (GRCm39)	I302N	probably benign	Het
Eif3a	C	T	19: 60,750,628 (GRCm39)	R1309Q	unknown	Het
Eno4	T	A	19: 58,935,084 (GRCm39)	Y100N	probably benign	Het
Ephx2	A	T	14: 66,349,602 (GRCm39)		probably null	Het
Fbxw14	A	T	9: 109,106,284 (GRCm39)	I251K	probably benign	Het
Fcgbp	T	C	7: 27,784,919 (GRCm39)		probably null	Het
Foxm1	A	C	6: 128,348,671 (GRCm39)		probably null	Het
Fscn3	T	A	6: 28,430,328 (GRCm39)	I166N	possibly damaging	Het
Gdpd4	G	T	7: 97,621,335 (GRCm39)	V193L	probably benign	Het
Gnpat	T	G	8: 125,606,869 (GRCm39)	C352G	probably benign	Het
H2-Q7	T	A	17: 35,658,910 (GRCm39)	Y120*	probably null	Het
Klri1	G	A	6: 129,694,070 (GRCm39)	R6C	probably benign	Het
Kmo	T	C	1: 175,476,729 (GRCm39)	V154A	probably benign	Het
Kmt2c	A	G	5: 25,559,685 (GRCm39)	L1031P	probably damaging	Het
Lrrc14b	T	G	13: 74,511,286 (GRCm39)	T265P	possibly damaging	Het
Lrrc2	C	T	9: 110,809,954 (GRCm39)	T330I	probably benign	Het
Lyn	T	A	4: 3,783,050 (GRCm39)	S428T	probably damaging	Het
Lypd10	T	A	7: 24,412,000 (GRCm39)	M60K	probably benign	Het
Mfsd8	T	A	3: 40,791,550 (GRCm39)	M59L	probably benign	Het
Mok	T	A	12: 110,774,799 (GRCm39)	Q341L	probably benign	Het
Muc21	T	C	17: 35,932,072 (GRCm39)	T705A	unknown	Het
Myh3	C	A	11: 66,979,856 (GRCm39)	N598K	probably benign	Het
Nbeal1	G	C	1: 60,276,310 (GRCm39)	V684L	probably benign	Het
Nlrp4e	A	G	7: 23,019,931 (GRCm39)	I139M	probably benign	Het
Or11g25	T	C	14: 50,723,692 (GRCm39)	V259A	probably benign	Het
Or3a10	T	A	11: 73,935,707 (GRCm39)	Q131L	possibly damaging	Het
Or4b13	G	A	2: 90,082,442 (GRCm39)	R297*	probably null	Het
Or51g2	A	G	7: 102,622,545 (GRCm39)	L218P	probably damaging	Het
Or52n2b	A	T	7: 104,565,619 (GRCm39)	Y295N	possibly damaging	Het
Osbpl7	G	A	11: 96,945,676 (GRCm39)	S312N	probably damaging	Het
Paxip1	A	G	5: 27,977,093 (GRCm39)	L323P	unknown	Het
Pcdh18	T	A	3: 49,699,684 (GRCm39)	H926L	probably damaging	Het
Pcm1	T	G	8: 41,763,153 (GRCm39)	S1460R	possibly damaging	Het
Pdha2	A	G	3: 140,917,155 (GRCm39)	S118P	possibly damaging	Het
Pdss1	A	T	2: 22,791,824 (GRCm39)	Y86F	probably benign	Het
Ppargc1a	A	T	5: 51,631,026 (GRCm39)	D534E	probably benign	Het
Prune2	A	G	19: 17,102,455 (GRCm39)	K2538R	probably benign	Het
Ptprq	A	T	10: 107,418,351 (GRCm39)	I1675N	probably damaging	Het
Rgma	C	T	7: 73,025,630 (GRCm39)	P3L	probably benign	Het
Ros1	A	G	10: 51,940,768 (GRCm39)		probably null	Het
Sema4g	C	T	19: 44,987,410 (GRCm39)	R519W	probably damaging	Het
Serpinc1	T	A	1: 160,820,971 (GRCm39)	F139L	probably damaging	Het
Slc22a29	A	G	19: 8,184,696 (GRCm39)	I198T	probably damaging	Het
Slc4a5	T	C	6: 83,280,373 (GRCm39)	V1007A	probably benign	Het
Sptbn1	T	C	11: 30,147,783 (GRCm39)	Y17C	possibly damaging	Het
Tex261	C	A	6: 83,751,999 (GRCm39)		probably null	Het
Timmdc1	T	A	16: 38,331,148 (GRCm39)	T128S	probably benign	Het
Tmem120b	C	A	5: 123,237,999 (GRCm39)	Y96*	probably null	Het
Tmem196	T	A	12: 119,982,311 (GRCm39)	F182I	possibly damaging	Het
Tnxb	G	A	17: 34,918,181 (GRCm39)	V2365M	possibly damaging	Het
Tph1	T	C	7: 46,303,233 (GRCm39)		silent	Het
Trmt9b	A	T	8: 36,978,857 (GRCm39)	K153N	probably damaging	Het
Trpc1	G	A	9: 95,592,323 (GRCm39)	Q551*	probably null	Het
Tubgcp3	T	C	8: 12,666,099 (GRCm39)	N828D	probably benign	Het
Unc13a	C	A	8: 72,108,933 (GRCm39)	G478W	probably damaging	Het
Usp15	T	A	10: 122,961,798 (GRCm39)	T627S		Het
Vmn1r115	A	T	7: 20,578,144 (GRCm39)	I256N	probably damaging	Het
Vmn2r6	T	A	3: 64,447,310 (GRCm39)	K585N	probably benign	Het
Vsir	G	T	10: 60,194,047 (GRCm39)		probably null	Het
Xirp2	A	G	2: 67,343,543 (GRCm39)	D1928G	probably benign	Het
Xylt1	A	G	7: 117,249,846 (GRCm39)	Y672C	probably damaging	Het
Zfc3h1	T	A	10: 115,254,616 (GRCm39)	N1403K	probably damaging	Het
Zfp160	A	T	17: 21,247,298 (GRCm39)	H616L	probably damaging	Het
Zfp637	T	A	6: 117,822,252 (GRCm39)	F127I	probably damaging	Het
Zfp69	G	T	4: 120,787,731 (GRCm39)	A528D	probably damaging	Het
Zpr1	T	A	9: 46,189,645 (GRCm39)	L342Q	possibly damaging	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
R3829:Yrdc	UTSW	4	124,745,554 (GRCm39)	start codon destroyed	probably null	0.92
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
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'- TCTCCTTCAAGTCGCCTGGG -3'
(R):5'- ACCAATCTCCAGTTCCGGATTC -3'

Sequencing Primer
(F):5'- TCGCGGTCCCTTTAAGCG -3'
(R):5'- AGTTCCGGATTCCTCCTCGG -3'

Posted On

2020-08-19