Mutagenetix > Incidental Mutation

Incidental Mutation 'R4461:Apex1'

330169

Institutional Source

Beutler Lab

Gene Symbol

Apex1

Ensembl Gene

ENSMUSG00000035960

Gene Name

apurinic/apyrimidinic endonuclease 1

Synonyms

Ref-1, HAP1

MMRRC Submission

041720-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4461 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

51162425-51164596 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 51163970 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 165 (V165A)

Ref Sequence

ENSEMBL: ENSMUSP00000123148 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000006452] [ENSMUST00000049312] [ENSMUST00000049411] [ENSMUST00000128395] [ENSMUST00000136753] [ENSMUST00000154288] [ENSMUST00000159292] [ENSMUST00000160375] [ENSMUST00000162957] [ENSMUST00000161166] [ENSMUST00000160890] [ENSMUST00000160393] [ENSMUST00000160538] [ENSMUST00000160835] [ENSMUST00000162177] [ENSMUST00000226871]

AlphaFold

P28352

Predicted Effect

probably benign
Transcript: ENSMUST00000006452

SMART Domains

Protein: ENSMUSP00000006452
Gene: ENSMUSG00000006289

Domain	Start	End	E-Value	Type
Pfam:Peptidase_M22	23	186	1.1e-55	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000049312

SMART Domains

Protein: ENSMUSP00000038276
Gene: ENSMUSG00000035953

Domain	Start	End	E-Value	Type
Pfam:Tmemb_55A	1	270	9.8e-132	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000049411
AA Change: V165A

PolyPhen 2 Score 0.676 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000042602
Gene: ENSMUSG00000035960
AA Change: V165A

Domain	Start	End	E-Value	Type
low complexity region	14	40	N/A	INTRINSIC
Pfam:Exo_endo_phos	64	308	1.5e-31	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000128395

SMART Domains

Protein: ENSMUSP00000116319
Gene: ENSMUSG00000035960

Domain	Start	End	E-Value	Type
low complexity region	9	35	N/A	INTRINSIC
Pfam:Exo_endo_phos	59	280	2.3e-24	PFAM
Pfam:Exo_endo_phos_2	138	284	4e-12	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000136753
AA Change: V165A

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000123148
Gene: ENSMUSG00000035960
AA Change: V165A

Domain	Start	End	E-Value	Type
low complexity region	14	40	N/A	INTRINSIC
Pfam:Exo_endo_phos	64	177	3.8e-13	PFAM

Predicted Effect

unknown
Transcript: ENSMUST00000154288
AA Change: V165A

SMART Domains

Protein: ENSMUSP00000122343
Gene: ENSMUSG00000035960
AA Change: V165A

Domain	Start	End	E-Value	Type
low complexity region	14	40	N/A	INTRINSIC
Pfam:Exo_endo_phos	64	214	1.1e-18	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000159047

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000159745

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000163043

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160464

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162935

Predicted Effect

probably benign
Transcript: ENSMUST00000159292

SMART Domains

Protein: ENSMUSP00000124039
Gene: ENSMUSG00000006289

Domain	Start	End	E-Value	Type
Pfam:Peptidase_M22	23	301	3.6e-90	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000160375

SMART Domains

Protein: ENSMUSP00000124099
Gene: ENSMUSG00000006289

Domain	Start	End	E-Value	Type
Pfam:Peptidase_M22	1	156	1.3e-45	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000162957

SMART Domains

Protein: ENSMUSP00000123697
Gene: ENSMUSG00000035953

Domain	Start	End	E-Value	Type
Pfam:Tmemb_55A	1	174	2.9e-64	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000161166

SMART Domains

Protein: ENSMUSP00000125414
Gene: ENSMUSG00000035953

Domain	Start	End	E-Value	Type
Pfam:Tmemb_55A	1	168	3.6e-65	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000160890

SMART Domains

Protein: ENSMUSP00000124659
Gene: ENSMUSG00000006289

Domain	Start	End	E-Value	Type
Pfam:Peptidase_M22	23	79	1.7e-14	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000161669

Predicted Effect

probably benign
Transcript: ENSMUST00000160393

SMART Domains

Protein: ENSMUSP00000125155
Gene: ENSMUSG00000006289

Domain	Start	End	E-Value	Type
Pfam:Peptidase_M22	23	301	3.6e-90	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000160538

SMART Domains

Protein: ENSMUSP00000124259
Gene: ENSMUSG00000035953

Domain	Start	End	E-Value	Type
Pfam:Tmemb_55A	1	197	1.9e-82	PFAM
low complexity region	221	235	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000160835

SMART Domains

Protein: ENSMUSP00000124782
Gene: ENSMUSG00000035953

Domain	Start	End	E-Value	Type
Pfam:Tmemb_55A	4	277	2.8e-129	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000162177

SMART Domains

Protein: ENSMUSP00000124016
Gene: ENSMUSG00000006289

Domain	Start	End	E-Value	Type
Pfam:Peptidase_M22	1	220	1.1e-68	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000163088

Predicted Effect

probably benign
Transcript: ENSMUST00000226871

Meta Mutation Damage Score

0.4163

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.1%
20x: 94.9%

Validation Efficiency

100% (50/50)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Apurinic/apyrimidinic (AP) sites occur frequently in DNA molecules by spontaneous hydrolysis, by DNA damaging agents or by DNA glycosylases that remove specific abnormal bases. AP sites are pre-mutagenic lesions that can prevent normal DNA replication so the cell contains systems to identify and repair such sites. Class II AP endonucleases cleave the phosphodiester backbone 5' to the AP site. This gene encodes the major AP endonuclease in human cells. Splice variants have been found for this gene; all encode the same protein. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality prior to E10 associated with abnormal embryogenesis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 45 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ankrd12	T	C	17: 66,292,932 (GRCm39)		probably null	Het
Btbd17	C	T	11: 114,684,815 (GRCm39)	D75N	possibly damaging	Het
Chd2	T	C	7: 73,190,622 (GRCm39)		probably benign	Het
Coq10a	T	C	10: 128,200,347 (GRCm39)	N138S	possibly damaging	Het
Ctbp1	A	T	5: 33,408,357 (GRCm39)	Y192N	probably damaging	Het
Cx3cl1	A	G	8: 95,507,184 (GRCm39)	*396W	probably null	Het
D6Ertd527e	T	C	6: 87,088,299 (GRCm39)	I154T	unknown	Het
Dao	T	A	5: 114,157,987 (GRCm39)	V203E	probably damaging	Het
Egr4	G	A	6: 85,489,322 (GRCm39)	A246V	probably damaging	Het
Gpsm1	G	A	2: 26,209,843 (GRCm39)		probably benign	Het
H2-Eb2	T	A	17: 34,552,497 (GRCm39)	V114E	possibly damaging	Het
Hpgds	A	G	6: 65,100,618 (GRCm39)	L120P	probably damaging	Het
Ikbke	C	T	1: 131,193,659 (GRCm39)	V464I	probably benign	Het
Kank2	G	A	9: 21,706,041 (GRCm39)	Q326*	probably null	Het
Klhl26	T	C	8: 70,904,194 (GRCm39)	Y538C	probably damaging	Het
Klkb1	A	G	8: 45,726,612 (GRCm39)	S464P	probably damaging	Het
Kmt2a	A	G	9: 44,760,263 (GRCm39)	Y529H	probably damaging	Het
Kmt2c	A	G	5: 25,504,874 (GRCm39)	V3478A	probably benign	Het
Knl1	A	C	2: 118,890,080 (GRCm39)	N44T	probably benign	Het
Letm2	A	G	8: 26,076,715 (GRCm39)	C296R	probably damaging	Het
Lrrc37a	A	G	11: 103,355,180 (GRCm39)		probably null	Het
Med20	T	C	17: 47,929,842 (GRCm39)	V93A	probably benign	Het
Mtmr11	T	C	3: 96,075,207 (GRCm39)		probably benign	Het
Muc1	A	T	3: 89,138,870 (GRCm39)	D493V	probably damaging	Het
Nek2	C	T	1: 191,554,827 (GRCm39)	P180S	probably damaging	Het
Nin	A	T	12: 70,089,359 (GRCm39)	M1352K	probably benign	Het
Or5aq1	T	C	2: 86,966,005 (GRCm39)	H220R	probably benign	Het
P3h3	A	T	6: 124,822,531 (GRCm39)	S547T	probably benign	Het
Pik3c2g	C	T	6: 139,787,407 (GRCm39)		probably benign	Het
Pkd1l3	A	G	8: 110,359,345 (GRCm39)		probably null	Het
Pzp	T	C	6: 128,501,003 (GRCm39)	I118M	probably benign	Het
Rps6ka5	C	A	12: 100,537,123 (GRCm39)	D536Y	probably damaging	Het
Rps6-ps2	A	G	8: 89,533,319 (GRCm39)		noncoding transcript	Het
Siglece	T	C	7: 43,300,929 (GRCm39)	Q462R	probably benign	Het
Sirt3	T	C	7: 140,444,913 (GRCm39)	D295G	possibly damaging	Het
Snph	G	A	2: 151,435,767 (GRCm39)	S318L	probably benign	Het
Snx18	T	C	13: 113,753,731 (GRCm39)	T401A	probably damaging	Het
Tefm	A	G	11: 80,028,875 (GRCm39)		probably null	Het
Thada	T	C	17: 84,733,665 (GRCm39)	Y994C	probably damaging	Het
Trmt1	A	G	8: 85,425,778 (GRCm39)	N531D	probably benign	Het
Ttc17	A	G	2: 94,196,916 (GRCm39)	V477A	probably benign	Het
Ubxn10	T	A	4: 138,448,187 (GRCm39)	Q163L	probably benign	Het
Ulk4	A	T	9: 120,985,950 (GRCm39)	I908N	possibly damaging	Het
Zfp747l1	A	G	7: 126,983,917 (GRCm39)	L395P	probably damaging	Het
Zscan12	C	T	13: 21,550,789 (GRCm39)	S136L	possibly damaging	Het

Other mutations in Apex1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01025:Apex1	APN	14	51,163,711 (GRCm39)	missense	possibly damaging	0.47
R3855:Apex1	UTSW	14	51,163,714 (GRCm39)	missense	probably benign	0.13
R3856:Apex1	UTSW	14	51,163,714 (GRCm39)	missense	probably benign	0.13
R6014:Apex1	UTSW	14	51,162,982 (GRCm39)	missense	probably benign	0.00
R6212:Apex1	UTSW	14	51,164,350 (GRCm39)	missense	probably benign	0.18
R7653:Apex1	UTSW	14	51,163,995 (GRCm39)	missense	probably damaging	1.00
R9206:Apex1	UTSW	14	51,163,125 (GRCm39)	missense	possibly damaging	0.81

Predicted Primers

PCR Primer
(F):5'- TCTCTTATGGCATTGGTGAGACC -3'
(R):5'- AGCAGTTCCCCAAAACCTTG -3'

Sequencing Primer
(F):5'- GCATTGGTGAGACCTTAATGAC -3'
(R):5'- AAAACCTTGGCGCTCCTG -3'

Posted On

2015-07-21