Mutagenetix > Incidental Mutation

Incidental Mutation 'R3856:Apex1'

276182

Institutional Source

Beutler Lab

Gene Symbol

Apex1

Ensembl Gene

ENSMUSG00000035960

Gene Name

apurinic/apyrimidinic endonuclease 1

Synonyms

Ref-1, HAP1

MMRRC Submission

040902-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R3856 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

51162425-51164596 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 51163714 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 109 (T109A)

Ref Sequence

ENSEMBL: ENSMUSP00000116319 (fasta)

Gene Model

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

probably benign
Transcript: ENSMUST00000049411
AA Change: T114A

PolyPhen 2 Score 0.066 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000042602
Gene: ENSMUSG00000035960
AA Change: T114A

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
AA Change: T109A

PolyPhen 2 Score 0.128 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000116319
Gene: ENSMUSG00000035960
AA Change: T109A

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 benign
Transcript: ENSMUST00000136753
AA Change: T114A

PolyPhen 2 Score 0.066 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000123148
Gene: ENSMUSG00000035960
AA Change: T114A

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: T114A

SMART Domains

Protein: ENSMUSP00000122343
Gene: ENSMUSG00000035960
AA Change: T114A

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: ENSMUST00000162935

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160464

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000159745

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000163043

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: 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: ENSMUST00000162177

SMART Domains

Protein: ENSMUSP00000124016
Gene: ENSMUSG00000006289

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

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: 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: 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: ENSMUST00000161166

SMART Domains

Protein: ENSMUSP00000125414
Gene: ENSMUSG00000035953

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000163088

Predicted Effect

probably benign
Transcript: ENSMUST00000226871

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.6%
3x: 98.7%
10x: 96.7%
20x: 92.4%

Validation Efficiency

100% (57/57)

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: 52 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acod1	T	C	14: 103,292,882 (GRCm39)	S469P	possibly damaging	Het
Adgrf5	A	T	17: 43,757,927 (GRCm39)	N787I	possibly damaging	Het
Ank2	T	C	3: 126,723,493 (GRCm39)	T945A	probably benign	Het
Aox4	T	A	1: 58,293,093 (GRCm39)	I863N	probably damaging	Het
Ap3d1	A	G	10: 80,548,019 (GRCm39)	I891T	probably benign	Het
Arhgef1	G	A	7: 24,618,697 (GRCm39)	G107S	probably damaging	Het
Atxn7l1	A	G	12: 33,417,599 (GRCm39)	T587A	probably damaging	Het
Atxn7l3	T	C	11: 102,184,729 (GRCm39)	D128G	probably damaging	Het
Cacna1h	T	C	17: 25,611,427 (GRCm39)	Y457C	probably damaging	Het
Ccdc60	A	C	5: 116,310,514 (GRCm39)	C183G	probably damaging	Het
Cep131	G	A	11: 119,958,011 (GRCm39)	R772*	probably null	Het
Cnst	C	T	1: 179,407,279 (GRCm39)	P109S	probably benign	Het
Crtc2	G	T	3: 90,169,877 (GRCm39)	L509F	probably damaging	Het
Ctsr	A	T	13: 61,309,750 (GRCm39)	I153N	possibly damaging	Het
Dffa	A	T	4: 149,188,708 (GRCm39)	M1L	possibly damaging	Het
Dnajc16	G	A	4: 141,490,964 (GRCm39)	R729*	probably null	Het
Eef2k	T	A	7: 120,498,594 (GRCm39)	C91*	probably null	Het
Eml5	T	C	12: 98,782,283 (GRCm39)	D1336G	probably damaging	Het
F12	G	A	13: 55,569,035 (GRCm39)		probably null	Het
Fam43b	G	C	4: 138,122,409 (GRCm39)	R304G	probably benign	Het
Fbxo40	A	T	16: 36,789,445 (GRCm39)	L555Q	probably damaging	Het
Frmpd1	T	C	4: 45,283,698 (GRCm39)	S840P	probably damaging	Het
Gadd45a	C	T	6: 67,013,989 (GRCm39)		probably null	Het
Galnt7	T	C	8: 57,985,658 (GRCm39)		probably benign	Het
Gm5592	G	A	7: 40,807,259 (GRCm39)		probably benign	Het
Gpr171	T	C	3: 59,005,506 (GRCm39)	T90A	probably damaging	Het
Gpr82	A	T	X: 13,531,577 (GRCm39)	T42S	probably benign	Het
H2-M10.6	T	A	17: 37,123,396 (GRCm39)	I30N	probably benign	Het
Hk2	T	C	6: 82,713,657 (GRCm39)	E447G	possibly damaging	Het
Hspa4l	C	A	3: 40,739,821 (GRCm39)	H698Q	probably benign	Het
Idi1	G	T	13: 8,935,968 (GRCm39)	A25S	probably benign	Het
Kdm4a	C	T	4: 118,010,428 (GRCm39)	R605H	probably damaging	Het
Nhlrc2	T	C	19: 56,576,703 (GRCm39)		probably null	Het
Nt5c2	A	G	19: 46,884,957 (GRCm39)	V252A	probably damaging	Het
Or52ae7	T	A	7: 103,119,867 (GRCm39)	V207E	probably damaging	Het
Pbp2	A	G	6: 135,287,143 (GRCm39)	L68P	probably benign	Het
Pcnx3	G	T	19: 5,728,995 (GRCm39)	T547K	probably benign	Het
Ppp1r12a	T	C	10: 108,089,362 (GRCm39)		probably benign	Het
Prmt9	G	A	8: 78,294,894 (GRCm39)	V413I	probably benign	Het
Pudp	T	C	18: 50,701,124 (GRCm39)	N203S	probably benign	Het
Rnf213	T	C	11: 119,371,765 (GRCm39)		probably benign	Het
Sall3	G	A	18: 81,015,717 (GRCm39)	T737M	probably damaging	Het
Scn2b	A	G	9: 45,036,759 (GRCm39)	N89S	possibly damaging	Het
Sgsm1	A	G	5: 113,411,125 (GRCm39)	V580A	probably benign	Het
Slc13a4	C	A	6: 35,248,539 (GRCm39)		probably null	Het
Slc4a4	A	C	5: 89,380,698 (GRCm39)	S1015R	probably benign	Het
Slc8a1	T	C	17: 81,955,803 (GRCm39)	T412A	probably benign	Het
Spag17	A	T	3: 100,014,075 (GRCm39)	D2116V	probably damaging	Het
Trim55	T	C	3: 19,727,120 (GRCm39)	F396L	probably benign	Het
Usp54	C	A	14: 20,638,488 (GRCm39)	M197I	probably damaging	Het
Vmn1r189	A	T	13: 22,286,439 (GRCm39)	F133I	possibly damaging	Het
Zfp735	T	C	11: 73,602,282 (GRCm39)	S409P	probably benign	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
R4461:Apex1	UTSW	14	51,163,970 (GRCm39)	missense	probably damaging	0.99
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'- ATATTCTGCTGCTCGAATGCC -3'
(R):5'- ACCCGGCCTTCTTGATCATG -3'

Sequencing Primer
(F):5'- AATGCCTTCTGTGTATAGCATGTAGC -3'
(R):5'- CTCGCCTATAAAAATAAAAACCAGTG -3'

Posted On

2015-04-06