Mutagenetix > Incidental Mutation

Incidental Mutation 'R7179:Prim1'

558850

Institutional Source

Beutler Lab

Gene Symbol

Prim1

Ensembl Gene

ENSMUSG00000025395

Gene Name

DNA primase, p49 subunit

Synonyms

MMRRC Submission

045269-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.963) question?

Stock #

R7179 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

127851084-127865899 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 127851845 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 39 (Y39C)

Ref Sequence

ENSEMBL: ENSMUSP00000026461 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000026461] [ENSMUST00000178041]

AlphaFold

P20664

Predicted Effect

probably damaging
Transcript: ENSMUST00000026461
AA Change: Y39C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000026461
Gene: ENSMUSG00000025395
AA Change: Y39C

Domain	Start	End	E-Value	Type
Pfam:DNA_primase_S	108	336	9.7e-59	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000178041
AA Change: Y39C

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000136556
Gene: ENSMUSG00000025395
AA Change: Y39C

Domain	Start	End	E-Value	Type
Pfam:DNA_primase_S	108	336	3.3e-71	PFAM

Meta Mutation Damage Score

0.3928

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.1%

Validation Efficiency

100% (76/76)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The replication of DNA in eukaryotic cells is carried out by a complex chromosomal replication apparatus, in which DNA polymerase alpha and primase are two key enzymatic components. Primase, which is a heterodimer of a small subunit and a large subunit, synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication. The protein encoded by this gene is the small, 49 kDa primase subunit. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acot13	A	T	13: 25,002,154 (GRCm39)	I96K	probably benign	Het
Adam6a	A	G	12: 113,509,291 (GRCm39)	T555A	probably benign	Het
Alms1	C	T	6: 85,598,351 (GRCm39)	P1059L	probably benign	Het
Apol7c	T	C	15: 77,409,843 (GRCm39)	T368A	probably benign	Het
Arfgef3	A	T	10: 18,475,015 (GRCm39)	L1557Q	probably damaging	Het
Baz2a	C	T	10: 127,960,326 (GRCm39)	R1514W	probably damaging	Het
Bmp3	T	A	5: 99,020,622 (GRCm39)	D348E	probably damaging	Het
Bves	A	G	10: 45,230,913 (GRCm39)	S295G	probably damaging	Het
Carmil1	A	G	13: 24,204,052 (GRCm39)	C1328R	probably benign	Het
Ccnk	T	A	12: 108,153,517 (GRCm39)	Y93N	probably damaging	Het
Ccr1	A	T	9: 123,764,089 (GRCm39)	V147D	probably damaging	Het
Cd24a	G	A	10: 43,458,636 (GRCm39)	G36S	probably benign	Het
Cep104	A	G	4: 154,077,324 (GRCm39)	Y569C	probably damaging	Het
Chd2	A	T	7: 73,125,168 (GRCm39)	I884N	probably damaging	Het
Cnst	A	T	1: 179,406,947 (GRCm39)		probably benign	Het
Col22a1	A	G	15: 71,805,262 (GRCm39)	L146P	unknown	Het
Col25a1	G	T	3: 130,323,768 (GRCm39)	R321L	probably damaging	Het
Ctnnd2	T	C	15: 30,683,510 (GRCm39)	Y504H	possibly damaging	Het
D3Ertd751e	C	A	3: 41,703,143 (GRCm39)	Q73K	probably damaging	Het
Dsc2	C	T	18: 20,168,332 (GRCm39)		probably null	Het
Eya1	A	T	1: 14,373,076 (GRCm39)	S14R	probably damaging	Het
Fam131c	A	T	4: 141,110,328 (GRCm39)		probably null	Het
Flvcr2	T	C	12: 85,793,965 (GRCm39)	F114L	possibly damaging	Het
Fyn	A	G	10: 39,408,120 (GRCm39)	D321G	possibly damaging	Het
Galnt5	A	C	2: 57,888,621 (GRCm39)	M74L	probably benign	Het
Garin4	G	A	1: 190,896,218 (GRCm39)	R142C	probably damaging	Het
Gas2l2	G	A	11: 83,313,288 (GRCm39)	P675S	probably benign	Het
Gm9508	G	T	10: 77,532,470 (GRCm39)	Q200K	unknown	Het
Greb1l	G	A	18: 10,544,576 (GRCm39)	S1390N	probably benign	Het
Hdac5	G	T	11: 102,095,385 (GRCm39)	T430K	possibly damaging	Het
Hjurp	TCTGGGAGGGCTTGCTCCGGGGGCAGTGTGTCCTGTTCTTGTGCAGCCCCTGCT	TCT	1: 88,194,000 (GRCm39)		probably benign	Het
Khnyn	C	T	14: 56,131,811 (GRCm39)	P578S	probably damaging	Het
Lepr	A	T	4: 101,602,856 (GRCm39)	T215S	probably benign	Het
Lrfn5	G	A	12: 61,890,768 (GRCm39)	V686I	probably benign	Het
Mapkap1	T	A	2: 34,408,712 (GRCm39)	H233Q	possibly damaging	Het
Mcm3	A	G	1: 20,885,081 (GRCm39)	I201T	probably damaging	Het
Metrnl	G	A	11: 121,606,734 (GRCm39)	R263Q	probably damaging	Het
Mettl22	A	G	16: 8,295,924 (GRCm39)	E71G	probably benign	Het
Muc16	T	C	9: 18,553,304 (GRCm39)	T4330A	probably benign	Het
Mug1	A	G	6: 121,834,379 (GRCm39)	T387A	probably benign	Het
Myh4	A	G	11: 67,135,550 (GRCm39)	D379G	probably benign	Het
Nbas	A	G	12: 13,455,398 (GRCm39)	D1204G	possibly damaging	Het
Ncor2	T	C	5: 125,132,847 (GRCm39)	K478E	unknown	Het
Or14a256	A	T	7: 86,265,574 (GRCm39)	L93Q	possibly damaging	Het
Or51d1	A	G	7: 102,347,477 (GRCm39)	T11A	probably benign	Het
Or5k1	T	A	16: 58,617,250 (GRCm39)	I320F	probably benign	Het
Osbpl7	G	A	11: 96,941,662 (GRCm39)	V62I	probably benign	Het
Pak1ip1	A	G	13: 41,163,018 (GRCm39)	N246S	probably damaging	Het
Prl3b1	G	T	13: 27,427,827 (GRCm39)	V46L	probably benign	Het
Prss54	A	T	8: 96,292,199 (GRCm39)	S127T	probably benign	Het
Rasal3	G	A	17: 32,611,391 (GRCm39)	T912M	probably damaging	Het
Rrp12	T	A	19: 41,872,217 (GRCm39)	T420S	probably benign	Het
Rspo1	A	G	4: 124,898,831 (GRCm39)	N51D	probably damaging	Het
Rufy4	A	G	1: 74,172,035 (GRCm39)	R253G	probably benign	Het
Scaf1	G	A	7: 44,657,167 (GRCm39)	R571C	unknown	Het
Scn2a	A	T	2: 65,532,323 (GRCm39)	H645L	probably damaging	Het
Sec24b	A	G	3: 129,782,595 (GRCm39)	S1132P	probably damaging	Het
Slc1a2	A	G	2: 102,586,290 (GRCm39)	K298R	probably damaging	Het
Slc25a54	T	A	3: 109,014,573 (GRCm39)	N230K	probably benign	Het
Slc27a4	T	G	2: 29,705,664 (GRCm39)	Y617*	probably null	Het
Slc2a10	T	C	2: 165,357,269 (GRCm39)	S310P	probably damaging	Het
Snx33	C	T	9: 56,833,151 (GRCm39)	R306H	probably damaging	Het
Spag9	A	T	11: 93,980,258 (GRCm39)		probably null	Het
Spg11	A	T	2: 121,932,270 (GRCm39)		probably null	Het
Sycp2l	A	G	13: 41,283,258 (GRCm39)	T165A	probably damaging	Het
Syt14	A	G	1: 192,615,571 (GRCm39)	C189R	probably damaging	Het
Taar9	A	T	10: 23,984,882 (GRCm39)	L184Q	probably damaging	Het
Tkt	C	T	14: 30,281,815 (GRCm39)	P111L	probably damaging	Het
Trpc1	A	T	9: 95,603,197 (GRCm39)	L445Q	possibly damaging	Het
Usp53	A	G	3: 122,743,359 (GRCm39)	S526P	probably benign	Het
Vps54	T	G	11: 21,248,791 (GRCm39)	W447G	probably damaging	Het
Xirp2	A	T	2: 67,340,177 (GRCm39)	H806L	probably benign	Het
Zfp451	A	T	1: 33,841,651 (GRCm39)	H410Q	unknown	Het
Zfp688	A	G	7: 127,018,484 (GRCm39)	C214R	probably damaging	Het
Zic4	A	G	9: 91,261,174 (GRCm39)	D143G	possibly damaging	Het

Other mutations in Prim1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01775:Prim1	APN	10	127,865,112 (GRCm39)	missense	probably benign
IGL01896:Prim1	APN	10	127,858,758 (GRCm39)	missense	probably damaging	1.00
IGL02505:Prim1	APN	10	127,865,652 (GRCm39)	makesense	probably null
PIT4403001:Prim1	UTSW	10	127,858,745 (GRCm39)	missense	probably benign	0.01
R0563:Prim1	UTSW	10	127,862,423 (GRCm39)	missense	probably damaging	1.00
R1732:Prim1	UTSW	10	127,851,193 (GRCm39)	missense	probably damaging	1.00
R1976:Prim1	UTSW	10	127,859,668 (GRCm39)	missense	probably benign
R2263:Prim1	UTSW	10	127,851,132 (GRCm39)	missense	probably benign	0.13
R4774:Prim1	UTSW	10	127,862,887 (GRCm39)	intron	probably benign
R4976:Prim1	UTSW	10	127,851,131 (GRCm39)	missense	probably damaging	0.97
R5908:Prim1	UTSW	10	127,853,893 (GRCm39)	missense	probably damaging	1.00
R6356:Prim1	UTSW	10	127,859,704 (GRCm39)	missense	probably damaging	0.97
R6598:Prim1	UTSW	10	127,856,049 (GRCm39)	missense	possibly damaging	0.83
R6794:Prim1	UTSW	10	127,854,018 (GRCm39)	missense	probably damaging	0.97
R7325:Prim1	UTSW	10	127,858,788 (GRCm39)	missense	probably null	0.13
R7432:Prim1	UTSW	10	127,851,885 (GRCm39)	missense	probably damaging	1.00
R7542:Prim1	UTSW	10	127,853,903 (GRCm39)	missense	probably damaging	1.00
R7659:Prim1	UTSW	10	127,862,458 (GRCm39)	critical splice donor site	probably null
R8382:Prim1	UTSW	10	127,856,138 (GRCm39)	splice site	probably null
R8828:Prim1	UTSW	10	127,859,761 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TCTAGAACAGAGCTGGGCAC -3'
(R):5'- GGCAAGGTATTTTCAGCCAAG -3'

Sequencing Primer
(F):5'- TTCATGAGTTCAAGGCGAGCC -3'
(R):5'- TACCTTCAAAACTTGGGGGC -3'

Posted On

2019-06-26