Mutagenetix > Incidental Mutation

Incidental Mutation 'R6940:Xndc1'

540498

Institutional Source

Beutler Lab

Gene Symbol

Xndc1

Ensembl Gene

ENSMUSG00000099481

Gene Name

Xrcc1 N-terminal domain containing 1

Synonyms

Xndr

MMRRC Submission

045054-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6940 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

101714718-101732972 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 101727094 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 161 (V161A)

Ref Sequence

ENSEMBL: ENSMUSP00000081903 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000084843] [ENSMUST00000094130] [ENSMUST00000106950] [ENSMUST00000123372] [ENSMUST00000139104] [ENSMUST00000142629] [ENSMUST00000146450]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000084843
AA Change: V161A

PolyPhen 2 Score 0.154 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000081903
Gene: ENSMUSG00000070425
AA Change: V161A

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 benign
Transcript: ENSMUST00000094130
AA Change: V161A

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000091680
Gene: ENSMUSG00000099481
AA Change: V161A

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: ENSMUST00000106950
AA Change: V161A

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000102563
Gene: ENSMUSG00000099481
AA Change: V161A

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: ENSMUST00000123372
AA Change: V161A

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000121068
Gene: ENSMUSG00000070425
AA Change: V161A

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
AA Change: V71A

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000122430
Gene: ENSMUSG00000070425
AA Change: V71A

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

Predicted Effect

probably benign
Transcript: ENSMUST00000142629

Predicted Effect

probably benign
Transcript: ENSMUST00000146450

SMART Domains

Protein: ENSMUSP00000117300
Gene: ENSMUSG00000099481

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

Predicted Effect

SMART Domains

Protein: ENSMUSP00000123466
Gene: ENSMUSG00000070425
AA Change: V72A

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.3%
20x: 97.8%

Validation Efficiency

100% (49/49)

Allele List at MGI

Other mutations in this stock

Total: 49 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acsbg1	C	A	9: 54,516,381 (GRCm39)	A667S	probably benign	Het
Ank2	G	A	3: 126,735,621 (GRCm39)		probably benign	Het
Arhgef28	A	G	13: 98,102,038 (GRCm39)	L812P	possibly damaging	Het
Armc5	C	T	7: 127,839,470 (GRCm39)	R263*	probably null	Het
Cadps2	A	T	6: 23,302,491 (GRCm39)	V740E	probably damaging	Het
Cckbr	T	C	7: 105,084,103 (GRCm39)	V279A	probably benign	Het
Cd101	T	C	3: 100,911,018 (GRCm39)	D880G	probably damaging	Het
Cep350	A	T	1: 155,804,297 (GRCm39)	S929T	probably benign	Het
Chaf1b	G	A	16: 93,702,853 (GRCm39)	R556H	probably benign	Het
Csn1s1	A	T	5: 87,822,882 (GRCm39)	Q69L	possibly damaging	Het
Dennd1b	T	C	1: 138,981,155 (GRCm39)		probably null	Het
Dnah11	T	C	12: 118,162,503 (GRCm39)	D22G	probably benign	Het
Dnah7a	T	C	1: 53,670,836 (GRCm39)	H472R	probably benign	Het
Dnah7b	G	A	1: 46,158,428 (GRCm39)	R337H	probably benign	Het
Eif2ak3	T	C	6: 70,869,386 (GRCm39)	V691A	possibly damaging	Het
Ern2	T	C	7: 121,785,369 (GRCm39)	R3G	probably benign	Het
Fat3	T	C	9: 15,828,096 (GRCm39)		probably null	Het
Fnbp4	T	C	2: 90,575,858 (GRCm39)	F20L	unknown	Het
Gtf2b	C	A	3: 142,484,016 (GRCm39)	D63E	probably damaging	Het
Hydin	A	G	8: 111,217,243 (GRCm39)	Y1377C	probably damaging	Het
Klf1	A	G	8: 85,628,724 (GRCm39)	T41A	possibly damaging	Het
Lce3d	G	A	3: 92,865,541 (GRCm39)	S52N	unknown	Het
Lrit1	G	C	14: 36,782,052 (GRCm39)	V242L	probably damaging	Het
Lrrfip1	T	A	1: 91,050,135 (GRCm39)		probably null	Het
Ltbp4	A	C	7: 27,008,369 (GRCm39)	V1313G	probably damaging	Het
Morc1	C	A	16: 48,300,208 (GRCm39)	S235*	probably null	Het
Mr1	T	G	1: 155,005,014 (GRCm39)	*342S	probably null	Het
Muc21	C	A	17: 35,934,118 (GRCm39)		probably benign	Het
Nol4l	T	A	2: 153,253,684 (GRCm39)	S630C	probably benign	Het
Nr4a3	C	T	4: 48,051,486 (GRCm39)	P80L	probably benign	Het
Or51a43	A	G	7: 103,717,620 (GRCm39)	I206T	possibly damaging	Het
Otof	A	G	5: 30,528,987 (GRCm39)	V1807A	probably damaging	Het
Pde5a	T	A	3: 122,572,681 (GRCm39)	V354E	possibly damaging	Het
Pmfbp1	A	T	8: 110,251,823 (GRCm39)	E355D	probably damaging	Het
Ppp2r2c	A	G	5: 37,084,875 (GRCm39)	D112G	probably damaging	Het
Prkacb	A	T	3: 146,457,254 (GRCm39)	I37N	probably damaging	Het
Prox2	T	C	12: 85,141,348 (GRCm39)	D285G	probably benign	Het
Ranbp3l	A	G	15: 9,041,792 (GRCm39)	S61G	probably benign	Het
Rnf214	T	A	9: 45,802,196 (GRCm39)	T289S	probably damaging	Het
Rnf217	G	T	10: 31,381,973 (GRCm39)		probably null	Het
Sc5d	A	T	9: 42,166,723 (GRCm39)	M272K	probably benign	Het
Slco6c1	T	C	1: 97,000,626 (GRCm39)	T542A	possibly damaging	Het
Sord	T	A	2: 122,094,536 (GRCm39)	I308N	probably damaging	Het
Syvn1	A	T	19: 6,101,214 (GRCm39)		probably benign	Het
Tas2r134	A	G	2: 51,518,148 (GRCm39)	H209R	probably benign	Het
Trak1	T	C	9: 121,272,784 (GRCm39)	V214A	possibly damaging	Het
Trpm5	C	A	7: 142,638,547 (GRCm39)	E322*	probably null	Het
Ttf2	T	C	3: 100,876,831 (GRCm39)	T17A	probably damaging	Het
Vmn2r53	T	C	7: 12,316,343 (GRCm39)	E492G	probably benign	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
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
R9230:Xndc1	UTSW	7	101,722,476 (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'- TTGCTCAAGCTCACACTTGC -3'
(R):5'- AGTCCCCTCTACCAAAAGGA -3'

Sequencing Primer
(F):5'- TTCCCAAGTGCTGAGATGAC -3'
(R):5'- CTGGAACTCACTTTGTAGACCAGG -3'

Posted On

2018-11-06