Mutagenetix > Incidental Mutation

Incidental Mutation 'R8802:Xndc1'

671558

Institutional Source

Beutler Lab

Gene Symbol

Xndc1

Ensembl Gene

ENSMUSG00000099481

Gene Name

Xrcc1 N-terminal domain containing 1

Synonyms

Xndr

MMRRC Submission

068639-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8802 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

101714718-101732972 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 101720539 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 6 (I6V)

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

possibly damaging
Transcript: ENSMUST00000084843
AA Change: I6V

PolyPhen 2 Score 0.456 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000081903
Gene: ENSMUSG00000070425
AA Change: I6V

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

possibly damaging
Transcript: ENSMUST00000094130
AA Change: I6V

PolyPhen 2 Score 0.842 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000091680
Gene: ENSMUSG00000099481
AA Change: I6V

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

possibly damaging
Transcript: ENSMUST00000106950
AA Change: I6V

PolyPhen 2 Score 0.842 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000102563
Gene: ENSMUSG00000099481
AA Change: I6V

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

possibly damaging
Transcript: ENSMUST00000123372
AA Change: I6V

PolyPhen 2 Score 0.842 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000121068
Gene: ENSMUSG00000070425
AA Change: I6V

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

possibly damaging
Transcript: ENSMUST00000146450
AA Change: I6V

PolyPhen 2 Score 0.842 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000117300
Gene: ENSMUSG00000099481
AA Change: I6V

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: 99.4%

Validation Efficiency

100% (59/59)

Allele List at MGI

Other mutations in this stock

Total: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2900092C05Rik	A	G	7: 12,249,415 (GRCm39)	T83A	possibly damaging	Het
Abcc6	A	G	7: 45,658,283 (GRCm39)	L451P	probably damaging	Het
Ak5	T	C	3: 152,321,631 (GRCm39)	E252G	probably damaging	Het
Atg4a-ps	T	A	3: 103,552,686 (GRCm39)	K218N	probably damaging	Het
Bglap2	T	A	3: 88,285,568 (GRCm39)	M35L	probably benign	Het
Bicral	A	G	17: 47,135,626 (GRCm39)	M528T	probably benign	Het
Cdh23	A	G	10: 60,244,877 (GRCm39)	V1008A	probably benign	Het
Chil6	A	T	3: 106,312,208 (GRCm39)	L31Q	probably damaging	Het
Ctnnd2	T	C	15: 30,967,022 (GRCm39)	V991A	probably damaging	Het
Dcc	T	C	18: 71,959,125 (GRCm39)	N216D	probably damaging	Het
Dcdc2c	T	A	12: 28,576,720 (GRCm39)	D106V	probably benign	Het
Dchs2	T	C	3: 83,253,544 (GRCm39)	I2318T	probably benign	Het
Fat2	A	G	11: 55,173,750 (GRCm39)	F2321S	possibly damaging	Het
Fbxw7	T	C	3: 84,859,693 (GRCm39)	V5A	unknown	Het
Fn3krp	T	C	11: 121,315,813 (GRCm39)	V68A	probably damaging	Het
Gcn1	T	C	5: 115,747,942 (GRCm39)	L1783P	probably damaging	Het
Gdf6	C	T	4: 9,844,769 (GRCm39)	H98Y	probably damaging	Het
Gm13271	C	A	4: 88,673,247 (GRCm39)	P48Q	probably damaging	Het
Gm4871	A	T	5: 144,966,876 (GRCm39)	N202K	probably benign	Het
Gucy1a2	G	A	9: 3,635,050 (GRCm39)	V365I	probably benign	Het
Hadhb	C	T	5: 30,378,831 (GRCm39)	Q157*	probably null	Het
Hivep2	C	T	10: 14,015,166 (GRCm39)	R1778C	probably damaging	Het
Hmcn2	T	A	2: 31,301,288 (GRCm39)	V2845E	probably damaging	Het
Hps3	T	A	3: 20,074,070 (GRCm39)	I431L	probably damaging	Het
Idh1	CA	CAA	1: 65,204,347 (GRCm39)		probably null	Het
Igkv12-38	A	T	6: 69,920,390 (GRCm39)	C43S	probably damaging	Het
Jph2	T	A	2: 163,239,184 (GRCm39)	H88L	probably damaging	Het
Kmt2b	G	A	7: 30,283,496 (GRCm39)	R955W	probably damaging	Het
Lrrc4c	A	G	2: 97,460,603 (GRCm39)	T410A	possibly damaging	Het
Ltf	C	T	9: 110,850,018 (GRCm39)	P14S	probably benign	Het
Mapk8ip3	G	A	17: 25,124,206 (GRCm39)	R521C	probably damaging	Het
Nampt	C	A	12: 32,900,435 (GRCm39)	T460K	probably benign	Het
Nek9	T	C	12: 85,374,192 (GRCm39)	I282V	probably benign	Het
Ninl	A	T	2: 150,777,172 (GRCm39)	V1394E	probably damaging	Het
Obox6	G	A	7: 15,567,772 (GRCm39)	S225L	probably damaging	Het
Or6k4	A	G	1: 173,964,616 (GRCm39)	Y102C	probably damaging	Het
Pcdha4	A	G	18: 37,087,211 (GRCm39)	K465E	possibly damaging	Het
Pex11g	T	C	8: 3,507,308 (GRCm39)	K151R	unknown	Het
Pld2	T	C	11: 70,446,824 (GRCm39)	L811P	probably damaging	Het
Pum2	C	T	12: 8,778,726 (GRCm39)	R459*	probably null	Het
Ralgapa1	T	C	12: 55,785,101 (GRCm39)	S720G	probably damaging	Het
Rbbp6	T	A	7: 122,587,680 (GRCm39)		probably benign	Het
Rbl1	A	G	2: 157,038,073 (GRCm39)		probably null	Het
Reln	G	T	5: 22,130,257 (GRCm39)	R2685S	probably damaging	Het
Rnf213	T	C	11: 119,352,928 (GRCm39)	F3942L		Het
Rpusd2	T	C	2: 118,865,378 (GRCm39)	V25A	probably benign	Het
Rusc1	T	A	3: 88,999,540 (GRCm39)	I81L	probably benign	Het
Serpinb9b	A	G	13: 33,213,587 (GRCm39)	E48G	probably benign	Het
Skil	C	T	3: 31,167,592 (GRCm39)	P408L	probably damaging	Het
Slc17a4	A	G	13: 24,089,274 (GRCm39)	W186R	probably damaging	Het
Syvn1	T	C	19: 6,097,968 (GRCm39)	F2S	probably benign	Het
Tmc6	T	C	11: 117,665,901 (GRCm39)	M338V	possibly damaging	Het
Tnfrsf17	A	T	16: 11,137,819 (GRCm39)	R185S	possibly damaging	Het
Utp20	T	C	10: 88,583,157 (GRCm39)	K2732R	probably damaging	Het
Vmn1r58	A	T	7: 5,414,080 (GRCm39)	V50E	probably damaging	Het
Vmn2r114	T	A	17: 23,528,836 (GRCm39)	D422V	possibly damaging	Het
Vmn2r83	A	T	10: 79,314,261 (GRCm39)	I170F	probably benign	Het
Xdh	C	T	17: 74,225,405 (GRCm39)	V466I	probably benign	Het
Zbtb38	T	C	9: 96,567,623 (GRCm39)	T1154A	probably benign	Het
Zfp160	T	A	17: 21,246,867 (GRCm39)	H472Q	probably damaging	Het
Zfp438	T	A	18: 5,213,417 (GRCm39)	T514S	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
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'- TAGCCCTGAGAAGTGAGGCTAC -3'
(R):5'- CCAAACTGCCATCTAGGGACTC -3'

Sequencing Primer
(F):5'- GTCTGCACAGAGAAACCGTTTTG -3'
(R):5'- CCATCTAGGGACTCTGGTATAGATAG -3'

Posted On

2021-04-30