Mutagenetix > Incidental Mutation

Incidental Mutation 'R9230:Xndc1'

700170

Institutional Source

Beutler Lab

Gene Symbol

Xndc1

Ensembl Gene

ENSMUSG00000099481

Gene Name

Xrcc1 N-terminal domain containing 1

Synonyms

Xndr

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9230 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

101714718-101732972 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 101722476 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glutamic Acid at position 47 (V47E)

Ref Sequence

ENSEMBL: ENSMUSP00000091680 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000084843] [ENSMUST00000094130] [ENSMUST00000106950] [ENSMUST00000123372] [ENSMUST00000139104] [ENSMUST00000146450]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000084843
AA Change: V47E

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

SMART Domains

Protein: ENSMUSP00000081903
Gene: ENSMUSG00000070425
AA Change: V47E

Domain	Start	End	E-Value	Type
Pfam:XRCC1_N	1	150	1.4e-54	PFAM
low complexity region	254	267	N/A	INTRINSIC
low complexity region	275	280	N/A	INTRINSIC
low complexity region	297	311	N/A	INTRINSIC
low complexity region	345	362	N/A	INTRINSIC
low complexity region	403	415	N/A	INTRINSIC
low complexity region	416	428	N/A	INTRINSIC
ANK	439	469	1.58e3	SMART
low complexity region	484	496	N/A	INTRINSIC
ANK	522	551	1.74e0	SMART
Pfam:TRP_2	557	619	1e-24	PFAM
Pfam:Ion_trans	716	1024	1.7e-24	PFAM
Pfam:PKD_channel	774	1019	2.4e-12	PFAM
low complexity region	1070	1081	N/A	INTRINSIC
low complexity region	1093	1104	N/A	INTRINSIC
coiled coil region	1122	1162	N/A	INTRINSIC
low complexity region	1220	1236	N/A	INTRINSIC
low complexity region	1247	1263	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000094130
AA Change: V47E

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

SMART Domains

Protein: ENSMUSP00000091680
Gene: ENSMUSG00000099481
AA Change: V47E

Domain	Start	End	E-Value	Type
Pfam:XRCC1_N	1	152	5.2e-29	PFAM
low complexity region	254	267	N/A	INTRINSIC
low complexity region	275	280	N/A	INTRINSIC
low complexity region	297	311	N/A	INTRINSIC
internal_repeat_1	324	345	2.69e-6	PROSPERO
low complexity region	346	379	N/A	INTRINSIC
internal_repeat_1	380	401	2.69e-6	PROSPERO

Predicted Effect

probably damaging
Transcript: ENSMUST00000106950
AA Change: V47E

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

SMART Domains

Protein: ENSMUSP00000102563
Gene: ENSMUSG00000099481
AA Change: V47E

Domain	Start	End	E-Value	Type
Pfam:XRCC1_N	1	152	5.2e-29	PFAM
low complexity region	254	267	N/A	INTRINSIC
low complexity region	275	280	N/A	INTRINSIC
low complexity region	297	311	N/A	INTRINSIC
internal_repeat_1	324	345	2.69e-6	PROSPERO
low complexity region	346	379	N/A	INTRINSIC
internal_repeat_1	380	401	2.69e-6	PROSPERO

Predicted Effect

probably damaging
Transcript: ENSMUST00000123372
AA Change: V47E

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

SMART Domains

Protein: ENSMUSP00000121068
Gene: ENSMUSG00000070425
AA Change: V47E

Domain	Start	End	E-Value	Type
Pfam:XRCC1_N	1	152	5.2e-29	PFAM
low complexity region	254	267	N/A	INTRINSIC
low complexity region	275	280	N/A	INTRINSIC
low complexity region	297	311	N/A	INTRINSIC
internal_repeat_1	324	345	2.69e-6	PROSPERO
low complexity region	346	379	N/A	INTRINSIC
internal_repeat_1	380	401	2.69e-6	PROSPERO

Predicted Effect

probably benign
Transcript: ENSMUST00000139104

SMART Domains

Protein: ENSMUSP00000122430
Gene: ENSMUSG00000070425

Domain	Start	End	E-Value	Type
Pfam:XRCC1_N	1	62	3.5e-14	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000146450
AA Change: V47E

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

SMART Domains

Protein: ENSMUSP00000117300
Gene: ENSMUSG00000099481
AA Change: V47E

Domain	Start	End	E-Value	Type
Pfam:XRCC1_N	1	152	1.1e-29	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000155078

SMART Domains

Protein: ENSMUSP00000123466
Gene: ENSMUSG00000070425

Domain	Start	End	E-Value	Type
Pfam:XRCC1_N	1	62	4.4e-22	PFAM

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

Validation Efficiency

100% (68/68)

Allele List at MGI

Other mutations in this stock

Total: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adarb1	A	T	10: 77,157,626 (GRCm39)	F274I	probably damaging	Het
Aen	T	A	7: 78,552,107 (GRCm39)	D22E	probably damaging	Het
Appl1	T	C	14: 26,645,692 (GRCm39)	E706G	unknown	Het
Arhgap21	T	C	2: 20,860,469 (GRCm39)	T1313A	possibly damaging	Het
Armc2	T	C	10: 41,823,935 (GRCm39)	Y511C	probably damaging	Het
Bsn	T	C	9: 107,989,459 (GRCm39)	T2098A	probably damaging	Het
Cacna1h	T	C	17: 25,599,856 (GRCm39)	Y1659C	probably damaging	Het
Catsperb	T	C	12: 101,516,053 (GRCm39)	I563T	probably benign	Het
Cblif	G	A	19: 11,737,748 (GRCm39)	W386*	probably null	Het
Cd180	TA	TAA	13: 102,841,514 (GRCm39)		probably null	Het
Cd55b	A	T	1: 130,350,619 (GRCm39)	L26*	probably null	Het
Cdc42bpa	A	G	1: 179,933,638 (GRCm39)	N759S	probably benign	Het
Chrm3	C	A	13: 9,928,479 (GRCm39)	V186L	probably benign	Het
Clrn2	A	G	5: 45,621,283 (GRCm39)	T226A	probably damaging	Het
Col3a1	C	T	1: 45,383,138 (GRCm39)	P1071S	unknown	Het
Csgalnact2	A	G	6: 118,103,212 (GRCm39)	L250P	probably damaging	Het
Cyp4a31	G	T	4: 115,428,281 (GRCm39)	E326*	probably null	Het
Def8	A	G	8: 124,186,317 (GRCm39)	E352G	probably benign	Het
Dmbt1	A	G	7: 130,639,642 (GRCm39)	D60G	probably benign	Het
Dock3	A	G	9: 106,807,223 (GRCm39)	L1368P	probably damaging	Het
Dytn	A	T	1: 63,686,611 (GRCm39)	V353D	probably benign	Het
Egfem1	G	A	3: 29,411,317 (GRCm39)	E155K	probably benign	Het
Eif3m	A	T	2: 104,831,705 (GRCm39)	M285K	probably damaging	Het
Fam135b	T	C	15: 71,335,856 (GRCm39)	K446R	probably benign	Het
Fbxo22	T	C	9: 55,116,442 (GRCm39)	L36P	probably damaging	Het
Frmd4a	T	C	2: 4,612,844 (GRCm39)	S1025P	possibly damaging	Het
Gja8	C	T	3: 96,826,664 (GRCm39)	V333M	possibly damaging	Het
Glis1	T	C	4: 107,425,327 (GRCm39)	S313P	probably benign	Het
Grid2ip	G	A	5: 143,359,194 (GRCm39)	R270Q	probably damaging	Het
Hps4	G	A	5: 112,525,905 (GRCm39)	S642N	possibly damaging	Het
Hspa4	T	C	11: 53,171,466 (GRCm39)	E246G	probably benign	Het
Ibtk	A	G	9: 85,585,702 (GRCm39)		probably null	Het
Ifit1	A	G	19: 34,625,236 (GRCm39)	E124G	possibly damaging	Het
Ifna14	T	C	4: 88,489,752 (GRCm39)	D95G	probably benign	Het
Igsf10	G	A	3: 59,243,843 (GRCm39)	R164W	probably damaging	Het
Ilkap	A	C	1: 91,314,937 (GRCm39)	I142S	probably benign	Het
Insyn2a	A	T	7: 134,520,439 (GRCm39)	Y30*	probably null	Het
Kctd14	C	G	7: 97,104,104 (GRCm39)	P53R	unknown	Het
Kndc1	A	T	7: 139,500,600 (GRCm39)	D655V	probably damaging	Het
Krt1c	A	C	15: 101,725,948 (GRCm39)	S197A	probably benign	Het
Lpin1	A	T	12: 16,588,483 (GRCm39)	S902R	unknown	Het
Mapk13	T	C	17: 28,994,532 (GRCm39)	I141T	probably damaging	Het
Micall2	A	G	5: 139,701,827 (GRCm39)	V472A	unknown	Het
Mmp15	T	C	8: 96,092,959 (GRCm39)	F113L	probably benign	Het
Msantd5f6	C	T	4: 73,319,685 (GRCm39)	A264T	probably benign	Het
Msh2	T	G	17: 88,026,717 (GRCm39)	S738A	probably benign	Het
Muc20	T	G	16: 32,613,584 (GRCm39)	T598P	probably damaging	Het
Myo1f	T	C	17: 33,795,424 (GRCm39)	V53A	probably damaging	Het
Ncf1	A	T	5: 134,250,718 (GRCm39)	N367K	probably benign	Het
Nme8	T	G	13: 19,874,384 (GRCm39)	I139L	probably benign	Het
Odam	T	C	5: 88,034,457 (GRCm39)	F46L	probably benign	Het
Or51a25	C	A	7: 102,372,795 (GRCm39)	V301F	possibly damaging	Het
Or7a42	G	A	10: 78,791,929 (GRCm39)	D297N	possibly damaging	Het
Pcare	A	G	17: 72,057,217 (GRCm39)	L820P	probably damaging	Het
Pi4ka	A	G	16: 17,099,788 (GRCm39)	I1945T		Het
Rbmyf9	T	G	Y: 3,774,819 (GRCm39)	D5E	probably damaging	Het
Rell1	T	C	5: 64,097,105 (GRCm39)		probably benign	Het
Ripk3	A	G	14: 56,023,303 (GRCm39)	F134S	probably benign	Het
Sclt1	A	T	3: 41,665,631 (GRCm39)	W146R	probably benign	Het
Slc18a2	T	C	19: 59,261,647 (GRCm39)	M178T	probably benign	Het
Slc24a5	G	T	2: 124,922,568 (GRCm39)	G110V	probably damaging	Het
Slc38a10	T	A	11: 119,996,781 (GRCm39)	D772V	probably benign	Het
Slc9c1	T	C	16: 45,398,275 (GRCm39)	L680P	possibly damaging	Het
Tll2	T	A	19: 41,093,436 (GRCm39)	Y477F	probably benign	Het
Tmco1	C	T	1: 167,136,132 (GRCm39)		probably benign	Het
Tnrc18	G	T	5: 142,773,392 (GRCm39)	A479D		Het
Topaz1	T	A	9: 122,596,097 (GRCm39)	M956K	probably benign	Het
Vmn2r56	T	A	7: 12,444,237 (GRCm39)	D465V	possibly damaging	Het

Other mutations in Xndc1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R0415:Xndc1	UTSW	7	101,729,823 (GRCm39)	splice site	probably benign
R0648:Xndc1	UTSW	7	101,728,031 (GRCm39)	missense	possibly damaging	0.46
R1990:Xndc1	UTSW	7	101,722,398 (GRCm39)	missense	probably damaging	1.00
R1991:Xndc1	UTSW	7	101,722,398 (GRCm39)	missense	probably damaging	1.00
R4290:Xndc1	UTSW	7	101,730,694 (GRCm39)	missense	possibly damaging	0.95
R4295:Xndc1	UTSW	7	101,730,694 (GRCm39)	missense	possibly damaging	0.95
R4530:Xndc1	UTSW	7	101,727,942 (GRCm39)	missense	probably benign	0.21
R4815:Xndc1	UTSW	7	101,722,523 (GRCm39)	missense	probably null	1.00
R5384:Xndc1	UTSW	7	101,731,395 (GRCm39)	missense	probably benign	0.12
R6838:Xndc1	UTSW	7	101,722,476 (GRCm39)	missense	possibly damaging	0.79
R6940:Xndc1	UTSW	7	101,727,094 (GRCm39)	missense	probably benign	0.15
R7310:Xndc1	UTSW	7	101,727,938 (GRCm39)	critical splice acceptor site	probably null
R7375:Xndc1	UTSW	7	101,730,687 (GRCm39)	splice site	probably null
R8271:Xndc1	UTSW	7	101,728,343 (GRCm39)	missense	possibly damaging	0.58
R8802:Xndc1	UTSW	7	101,720,539 (GRCm39)	missense	possibly damaging	0.84
R8876:Xndc1	UTSW	7	101,729,754 (GRCm39)	missense	probably benign	0.06
R8996:Xndc1	UTSW	7	101,722,518 (GRCm39)	missense	probably damaging	1.00
R9716:Xndc1	UTSW	7	101,725,114 (GRCm39)	missense	probably damaging	1.00
X0060:Xndc1	UTSW	7	101,728,355 (GRCm39)	missense	probably benign	0.08
X0065:Xndc1	UTSW	7	101,730,692 (GRCm39)	missense	probably benign	0.03

Predicted Primers

PCR Primer
(F):5'- TCAGCAGGTCTGGAATTGTAGG -3'
(R):5'- CTGGGTTTCTTCAGCACCAAG -3'

Sequencing Primer
(F):5'- AGCAGGTCTGGAATTGTAGGTATCTC -3'
(R):5'- GGGTAAAGAGCACATTGTCTCCTC -3'

Posted On

2022-02-07