Mutagenetix > Incidental Mutation

Incidental Mutation 'R0648:Xndc1'

57345

Institutional Source

Beutler Lab

Gene Symbol

Xndc1

Ensembl Gene

ENSMUSG00000099481

Gene Name

Xrcc1 N-terminal domain containing 1

Synonyms

Xndr

MMRRC Submission

038833-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0648 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

101714718-101732972 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 101728031 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 14 (V14A)

Ref Sequence

ENSEMBL: ENSMUSP00000121475 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000084843] [ENSMUST00000094129] [ENSMUST00000094130] [ENSMUST00000106950] [ENSMUST00000123372] [ENSMUST00000124189] [ENSMUST00000139104] [ENSMUST00000142629] [ENSMUST00000146450]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000084843

SMART Domains

Protein: ENSMUSP00000081903
Gene: ENSMUSG00000070425

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: ENSMUST00000094129

SMART Domains

Protein: ENSMUSP00000091679
Gene: ENSMUSG00000070425

Domain	Start	End	E-Value	Type
Pfam:XRCC1_N	1	152	1.2e-27	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	2.8e-28	PFAM
transmembrane domain	719	741	N/A	INTRINSIC
Pfam:PKD_channel	772	1019	3.8e-12	PFAM
Pfam:Ion_trans	796	1012	3.9e-31	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

SMART Domains

Protein: ENSMUSP00000091680
Gene: ENSMUSG00000099481

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

SMART Domains

Protein: ENSMUSP00000102563
Gene: ENSMUSG00000099481

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

SMART Domains

Protein: ENSMUSP00000121068
Gene: ENSMUSG00000070425

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: ENSMUST00000124189

SMART Domains

Protein: ENSMUSP00000116934
Gene: ENSMUSG00000100254

Domain	Start	End	E-Value	Type
low complexity region	29	41	N/A	INTRINSIC
low complexity region	42	54	N/A	INTRINSIC
ANK	65	95	1.58e3	SMART
low complexity region	110	122	N/A	INTRINSIC
ANK	148	177	1.74e0	SMART
Pfam:TRP_2	183	245	9.1e-29	PFAM
transmembrane domain	345	367	N/A	INTRINSIC
Pfam:PKD_channel	398	645	1.4e-12	PFAM
Pfam:Ion_trans	422	638	1e-31	PFAM
low complexity region	696	707	N/A	INTRINSIC
low complexity region	719	730	N/A	INTRINSIC
coiled coil region	748	788	N/A	INTRINSIC
low complexity region	846	862	N/A	INTRINSIC
low complexity region	873	889	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000125197

Predicted Effect

probably benign
Transcript: ENSMUST00000139104
AA Change: V115A

PolyPhen 2 Score 0.166 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000122430
Gene: ENSMUSG00000070425
AA Change: V115A

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000142629
AA Change: V14A

PolyPhen 2 Score 0.455 (Sensitivity: 0.89; Specificity: 0.90)

Predicted Effect

unknown
Transcript: ENSMUST00000155078
AA Change: V116A

SMART Domains

Protein: ENSMUSP00000123466
Gene: ENSMUSG00000070425
AA Change: V116A

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153176

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000143839

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000140395

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

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.6%
20x: 96.0%

Validation Efficiency

100% (80/80)

Allele List at MGI

Other mutations in this stock

Total: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc5	A	G	16: 20,184,632 (GRCm39)	V1009A	possibly damaging	Het
Acta2	T	C	19: 34,225,934 (GRCm39)	I87V	probably benign	Het
Arid1a	A	G	4: 133,412,515 (GRCm39)	Y1560H	unknown	Het
Bcor	C	T	X: 11,925,290 (GRCm39)	R102Q	probably damaging	Het
Camsap2	A	T	1: 136,232,057 (GRCm39)	D179E	probably damaging	Het
Ccdc168	A	G	1: 44,095,723 (GRCm39)	S1792P	possibly damaging	Het
Ccdc18	T	A	5: 108,283,426 (GRCm39)	S46T	probably damaging	Het
Ccdc18	A	C	5: 108,322,853 (GRCm39)	Q651P	probably damaging	Het
Cdc73	T	C	1: 143,571,200 (GRCm39)	T80A	probably benign	Het
Cdh20	T	A	1: 109,993,337 (GRCm39)		probably benign	Het
Cenpe	G	A	3: 134,935,843 (GRCm39)	G426D	probably damaging	Het
Cenpt	A	G	8: 106,571,592 (GRCm39)	V487A	probably damaging	Het
Clec2m	A	G	6: 129,307,932 (GRCm39)	F46L	probably benign	Het
Col4a1	G	A	8: 11,296,892 (GRCm39)	P84S	unknown	Het
Dennd2d	A	G	3: 106,407,871 (GRCm39)	I450M	probably damaging	Het
Dhps	C	A	8: 85,799,911 (GRCm39)		probably null	Het
Ebf1	A	T	11: 44,882,337 (GRCm39)	H431L	probably damaging	Het
Efcab6	A	G	15: 83,817,265 (GRCm39)		probably benign	Het
Egflam	T	C	15: 7,237,190 (GRCm39)	H990R	probably damaging	Het
Ercc6l2	A	G	13: 63,992,459 (GRCm39)	T303A	probably benign	Het
Fam167b	T	C	4: 129,472,150 (GRCm39)	K7E	probably benign	Het
Fgd3	T	C	13: 49,450,049 (GRCm39)	I67V	probably benign	Het
Fhip1a	A	C	3: 85,637,921 (GRCm39)	V126G	probably damaging	Het
Fn1	A	T	1: 71,636,744 (GRCm39)	V2045D	possibly damaging	Het
Gnl1	A	G	17: 36,293,490 (GRCm39)	N225S	probably damaging	Het
Gpx6	A	T	13: 21,503,047 (GRCm39)	N154Y	probably benign	Het
H2bc21	A	G	3: 96,128,851 (GRCm39)	S124G	probably benign	Het
Haus8	C	A	8: 71,709,174 (GRCm39)	G79V	probably damaging	Het
Hdgfl1	A	T	13: 26,953,836 (GRCm39)	L79Q	probably damaging	Het
Impdh2	T	C	9: 108,440,665 (GRCm39)	Y83H	probably benign	Het
Lama2	T	C	10: 26,865,372 (GRCm39)	T2929A	probably benign	Het
Lpin2	T	C	17: 71,536,307 (GRCm39)	S199P	probably benign	Het
Moap1	T	C	12: 102,708,776 (GRCm39)	T258A	probably benign	Het
Mrps35	C	A	6: 146,957,443 (GRCm39)	S156*	probably null	Het
Mrtfa	A	G	15: 80,901,121 (GRCm39)	S457P	probably damaging	Het
Mtbp	C	T	15: 55,466,597 (GRCm39)	P537S	probably benign	Het
Ncstn	C	A	1: 171,895,454 (GRCm39)	V565F	probably benign	Het
Nhsl1	A	G	10: 18,407,474 (GRCm39)	N1536S	possibly damaging	Het
Nkain4	T	C	2: 180,584,905 (GRCm39)	Q103R	possibly damaging	Het
Nsun2	T	A	13: 69,775,706 (GRCm39)	N383K	probably damaging	Het
Or13p4	C	T	4: 118,547,269 (GRCm39)	V127I	probably benign	Het
Or6c33	A	G	10: 129,853,350 (GRCm39)	N40S	probably damaging	Het
Parp1	C	T	1: 180,428,005 (GRCm39)		probably benign	Het
Pkd1	G	A	17: 24,813,911 (GRCm39)	R4125H	probably damaging	Het
Plxnd1	T	C	6: 115,970,962 (GRCm39)	I269V	possibly damaging	Het
Polr1f	C	T	12: 33,487,999 (GRCm39)	Q305*	probably null	Het
Ppp1r36dn	A	G	12: 76,498,070 (GRCm39)		noncoding transcript	Het
Qrich1	T	A	9: 108,422,076 (GRCm39)	N563K	probably damaging	Het
Rab3il1	TGAAG	TGAAGAAG	19: 10,004,752 (GRCm39)		probably benign	Het
Rell1	G	A	5: 64,082,088 (GRCm39)	T271M	probably benign	Het
Rgl1	A	G	1: 152,412,016 (GRCm39)		probably null	Het
Rph3a	C	T	5: 121,097,333 (GRCm39)	R261H	possibly damaging	Het
Ryr2	A	T	13: 11,739,219 (GRCm39)	M2161K	possibly damaging	Het
Scaf11	T	C	15: 96,316,339 (GRCm39)	N1075S	possibly damaging	Het
Serpina3j	A	G	12: 104,280,938 (GRCm39)	D37G	probably benign	Het
Siah2	A	G	3: 58,583,635 (GRCm39)	V217A	probably damaging	Het
Sik2	T	C	9: 50,810,045 (GRCm39)	D506G	probably benign	Het
Skap2	A	C	6: 51,856,765 (GRCm39)	V279G	probably benign	Het
Slc8a3	G	T	12: 81,361,220 (GRCm39)	T533N	probably damaging	Het
Slc9a7	A	T	X: 20,028,659 (GRCm39)		probably benign	Het
Snai3	G	T	8: 123,181,733 (GRCm39)	F241L	probably damaging	Het
Speg	T	C	1: 75,404,622 (GRCm39)	S2805P	probably benign	Het
Spink5	A	T	18: 44,132,864 (GRCm39)		probably benign	Het
Tctn1	C	T	5: 122,389,761 (GRCm39)	E254K	probably benign	Het
Tdrd3	C	T	14: 87,709,618 (GRCm39)	T100M	probably damaging	Het
Tex47	T	C	5: 7,355,215 (GRCm39)	V132A	probably benign	Het
Thbs3	A	G	3: 89,123,972 (GRCm39)		probably null	Het
Tigit	T	A	16: 43,482,401 (GRCm39)	Y111F	probably damaging	Het
Tmem245	A	G	4: 56,906,270 (GRCm39)	I148T	probably benign	Het
Tmem97	A	G	11: 78,441,365 (GRCm39)	Y39H	probably benign	Het
Tnks2	T	A	19: 36,839,474 (GRCm39)		probably null	Het
Trp53bp1	A	G	2: 121,066,188 (GRCm39)	V846A	probably benign	Het
Tulp2	T	G	7: 45,169,210 (GRCm39)	I259S	probably damaging	Het
Ubxn1	G	A	19: 8,851,612 (GRCm39)	R215H	probably damaging	Het
Vmn1r17	A	G	6: 57,337,460 (GRCm39)	F253L	probably damaging	Het
Vmn2r10	T	C	5: 109,143,782 (GRCm39)	M723V	probably benign	Het
Xpnpep1	A	G	19: 52,986,294 (GRCm39)		probably benign	Het
Yes1	T	A	5: 32,812,862 (GRCm39)	M322K	possibly damaging	Het
Zdhhc14	C	A	17: 5,543,877 (GRCm39)	N52K	probably benign	Het
Zfp42	A	G	8: 43,749,015 (GRCm39)	V162A	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
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
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'- CCCTTCTGATCCTGACAAAACCCTG -3'
(R):5'- CTGGCTGCAACTGCTTCAACATAC -3'

Sequencing Primer
(F):5'- TAGATTGCTCACGGCAGATAC -3'
(R):5'- GCAACTGCTTCAACATACCCTTG -3'

Posted On

2013-07-11