Mutagenetix > Incidental Mutation

Incidental Mutation 'R9159:Yrdc'

695559

Institutional Source

Beutler Lab

Gene Symbol

Yrdc

Ensembl Gene

ENSMUSG00000028889

Gene Name

yrdC domain containing (E.coli)

Synonyms

IRIP

MMRRC Submission

Accession Numbers

Essential gene?

Probably essential (E-score: 0.961) question?

Stock #

R9159 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

124744552-124749035 bp(+) (GRCm39)

Type of Mutation

critical splice donor site (2 bp from exon)

DNA Base Change (assembly)

T to C at 124747811 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

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 null
Transcript: ENSMUST00000102628

SMART Domains

Protein: ENSMUSP00000099688
Gene: ENSMUSG00000028889

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.2%

Validation Efficiency

97% (72/74)

Allele List at MGI

Other mutations in this stock

Total: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9930012K11Rik	A	T	14: 70,394,238 (GRCm39)	M179K	probably benign	Het
A030003K21Rik	A	G	1: 82,920,787 (GRCm39)	V86A	unknown	Het
AC133488.1	A	T	16: 18,440,075 (GRCm39)	V363E	probably benign	Het
Adamts16	A	G	13: 70,901,408 (GRCm39)	S890P	probably benign	Het
Adgrf4	A	G	17: 42,973,293 (GRCm39)	V685A	probably benign	Het
Aff1	T	A	5: 103,990,131 (GRCm39)	M867K	possibly damaging	Het
Apba3	T	A	10: 81,106,867 (GRCm39)	S225T		Het
Aplp1	T	A	7: 30,141,775 (GRCm39)	T228S	probably benign	Het
Arhgap18	A	G	10: 26,730,886 (GRCm39)	D188G	probably benign	Het
BC024063	T	A	10: 81,944,906 (GRCm39)	S175R	possibly damaging	Het
Bloc1s6	T	G	2: 122,580,548 (GRCm39)	S2R	probably damaging	Het
Cd209b	A	G	8: 3,974,245 (GRCm39)	I119T	possibly damaging	Het
Cdk8	T	C	5: 146,168,549 (GRCm39)	V16A	probably damaging	Het
Cep295	A	G	9: 15,252,904 (GRCm39)	M308T	probably benign	Het
Cfap53	T	A	18: 74,416,272 (GRCm39)	Y2N	probably damaging	Het
Col28a1	T	A	6: 8,014,993 (GRCm39)	D804V	probably damaging	Het
Csta3	G	A	16: 36,038,069 (GRCm39)	V69I	probably benign	Het
Cyp2c40	A	T	19: 39,762,317 (GRCm39)	D443E	probably damaging	Het
Cyp2d9	A	G	15: 82,338,572 (GRCm39)	D202G	possibly damaging	Het
Dchs1	G	A	7: 105,415,126 (GRCm39)	A686V	probably benign	Het
Egf	A	T	3: 129,472,026 (GRCm39)	N1199K	probably benign	Het
Eva1a	A	G	6: 82,068,855 (GRCm39)	R61G	possibly damaging	Het
Exoc6	T	A	19: 37,597,478 (GRCm39)	D626E	probably benign	Het
Exosc10	T	C	4: 148,663,916 (GRCm39)		probably null	Het
Firrm	A	G	1: 163,814,514 (GRCm39)	I143T	probably damaging	Het
Gm12888	T	C	4: 121,176,600 (GRCm39)	Q67R	probably null	Het
Gm16485	A	G	9: 8,972,319 (GRCm39)	S62G	unknown	Het
Gng4	T	C	13: 13,999,896 (GRCm39)	I55T	probably damaging	Het
Gpihbp1	A	G	15: 75,469,830 (GRCm39)	S182G	possibly damaging	Het
Hax1	T	C	3: 89,903,127 (GRCm39)	R251G	probably damaging	Het
Igf2bp2	G	A	16: 21,900,502 (GRCm39)	T213I	probably damaging	Het
Il23a	T	A	10: 128,133,427 (GRCm39)	K66*	probably null	Het
Itga2	A	T	13: 115,014,298 (GRCm39)	L210*	probably null	Het
Ltbp2	G	A	12: 84,837,864 (GRCm39)	P1192L	probably benign	Het
Matr3	T	A	18: 35,712,355 (GRCm39)	M389K	possibly damaging	Het
Mettl15	T	C	2: 108,923,444 (GRCm39)	D326G	probably damaging	Het
Mta1	T	A	12: 113,100,025 (GRCm39)	V645E	probably damaging	Het
Muc5ac	T	C	7: 141,363,529 (GRCm39)	I2280T	unknown	Het
Naa15	T	A	3: 51,358,802 (GRCm39)	N362K	probably benign	Het
Necab2	T	C	8: 120,189,303 (GRCm39)	Y158H	probably damaging	Het
Nphp3	T	A	9: 103,897,980 (GRCm39)	L523Q	probably damaging	Het
Nphs1	T	G	7: 30,165,026 (GRCm39)	F540V	possibly damaging	Het
Or2av9	A	G	11: 58,381,350 (GRCm39)	V77A	probably damaging	Het
Or2k2	A	G	4: 58,785,320 (GRCm39)	I134T	probably benign	Het
Or5p55	A	T	7: 107,567,524 (GRCm39)	R307*	probably null	Het
Ppa1	A	T	10: 61,496,784 (GRCm39)	I91F	probably damaging	Het
Prdm6	C	A	18: 53,598,019 (GRCm39)	A127D	unknown	Het
Prdm8	T	C	5: 98,334,175 (GRCm39)	F581L	probably damaging	Het
Rbbp6	T	C	7: 122,589,428 (GRCm39)	I372T	probably damaging	Het
Rnf144b	A	G	13: 47,396,348 (GRCm39)	I228M	probably damaging	Het
Rsf1	CG	CGACGGCGGGG	7: 97,229,115 (GRCm39)		probably benign	Het
Setd2	T	C	9: 110,374,385 (GRCm39)		probably null	Het
Sez6l	T	C	5: 112,613,824 (GRCm39)	H441R	possibly damaging	Het
Shbg	G	A	11: 69,506,430 (GRCm39)	L327F	probably benign	Het
Sik3	C	T	9: 46,123,539 (GRCm39)	Q1113*	probably null	Het
Smad2	T	A	18: 76,395,573 (GRCm39)	I4N	possibly damaging	Het
Spata31h1	G	A	10: 82,118,524 (GRCm39)	R4829*	probably null	Het
Sult2b1	T	A	7: 45,391,534 (GRCm39)	E84V	probably damaging	Het
Tbc1d8	A	G	1: 39,444,474 (GRCm39)	Y162H		Het
Tedc2	A	G	17: 24,436,705 (GRCm39)	L308P	probably damaging	Het
Tmc5	T	C	7: 118,233,264 (GRCm39)	V26A	probably benign	Het
Tmem120b	T	A	5: 123,242,566 (GRCm39)	N181K	possibly damaging	Het
Tmem229b	T	G	12: 79,011,448 (GRCm39)	N161T	possibly damaging	Het
Tmem43	A	C	6: 91,459,291 (GRCm39)	D254A	probably benign	Het
Trpv6	T	C	6: 41,603,074 (GRCm39)	D266G	probably benign	Het
Tspan9	A	G	6: 127,943,717 (GRCm39)	I102T	possibly damaging	Het
Ung	A	G	5: 114,270,166 (GRCm39)		probably benign	Het
Upp2	C	T	2: 58,667,996 (GRCm39)	H230Y	probably damaging	Het
Vmn1r184	G	A	7: 25,966,545 (GRCm39)	S97N	possibly damaging	Het
Vmn2r73	A	T	7: 85,521,931 (GRCm39)	V136E	possibly damaging	Het
Wdr20rt	T	C	12: 65,272,918 (GRCm39)	V127A	probably damaging	Het
Yme1l1	T	A	2: 23,063,058 (GRCm39)	F210I	probably damaging	Het
Zfhx4	G	T	3: 5,464,312 (GRCm39)	R1515L	probably damaging	Het
Zfhx4	C	T	3: 5,466,217 (GRCm39)	P2150L	probably damaging	Het
Zfp267	C	A	3: 36,219,902 (GRCm39)	H642N	possibly damaging	Het
Zfp988	C	T	4: 147,416,450 (GRCm39)	P295S	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
R8169:Yrdc	UTSW	4	124,744,880 (GRCm39)	missense	probably benign
R8837:Yrdc	UTSW	4	124,747,677 (GRCm39)	missense	probably benign	0.01
Z1176:Yrdc	UTSW	4	124,745,290 (GRCm39)	unclassified	probably benign

Predicted Primers

PCR Primer
(F):5'- AATTCAGCTGTGCCCTAACC -3'
(R):5'- CCTTAGTGGTCCCTTTAAAATGG -3'

Sequencing Primer
(F):5'- CTTCTTTCTTTTCAGGAGTTCCAAG -3'
(R):5'- CAAGACAGGGTTTCTATGTGTAGCC -3'

Posted On

2022-01-20