Mutagenetix > Incidental Mutation

Incidental Mutation 'R1976:Prim1'

221744

Institutional Source

Beutler Lab

Gene Symbol

Prim1

Ensembl Gene

ENSMUSG00000025395

Gene Name

DNA primase, p49 subunit

Synonyms

MMRRC Submission

039989-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.963) question?

Stock #

R1976 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

127851084-127865899 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 127859668 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Serine at position 288 (C288S)

Ref Sequence

ENSEMBL: ENSMUSP00000136556 (fasta)

Gene Model

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

AlphaFold

P20664

Predicted Effect

probably benign
Transcript: ENSMUST00000026461
AA Change: C287S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000026461
Gene: ENSMUSG00000025395
AA Change: C287S

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000133285

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000135580

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138330

Predicted Effect

probably benign
Transcript: ENSMUST00000178041
AA Change: C288S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000136556
Gene: ENSMUSG00000025395
AA Change: C288S

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

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.0%
20x: 94.8%

Validation Efficiency

98% (65/66)

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: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	T	C	11: 9,347,815 (GRCm39)	V3556A	probably damaging	Het
Abcb5	T	C	12: 118,854,417 (GRCm39)	I833V	probably benign	Het
Adgrd1	A	T	5: 129,217,861 (GRCm39)	H432L	probably benign	Het
Alppl2	T	A	1: 87,016,463 (GRCm39)	I204F	probably damaging	Het
Ascc3	T	A	10: 50,525,262 (GRCm39)	F486I	probably damaging	Het
Bcl9l	T	A	9: 44,417,449 (GRCm39)	L429Q	possibly damaging	Het
Ccdc33	A	T	9: 58,024,445 (GRCm39)	Y227*	probably null	Het
Cd101	A	G	3: 100,915,377 (GRCm39)	V730A	probably damaging	Het
Cdadc1	A	T	14: 59,811,217 (GRCm39)	V431E	probably damaging	Het
Dazap1	T	A	10: 80,110,454 (GRCm39)		probably null	Het
Dbpht2	T	A	12: 74,342,635 (GRCm39)		noncoding transcript	Het
Dennd4b	A	T	3: 90,180,362 (GRCm39)	T742S	probably damaging	Het
Dhtkd1	T	C	2: 5,907,202 (GRCm39)	E838G	possibly damaging	Het
Dync2h1	A	T	9: 7,129,045 (GRCm39)	D1823E	probably benign	Het
Enox1	T	A	14: 77,906,233 (GRCm39)	N556K	probably benign	Het
Fam227a	T	C	15: 79,510,477 (GRCm39)	I392M	possibly damaging	Het
Fnip2	A	T	3: 79,388,238 (GRCm39)	M831K	probably benign	Het
Foxn1	T	C	11: 78,256,763 (GRCm39)		probably benign	Het
Garre1	A	C	7: 33,956,805 (GRCm39)	N353K	probably damaging	Het
Glis3	T	C	19: 28,240,077 (GRCm39)	936	probably benign	Het
Gm4953	T	A	1: 158,995,923 (GRCm39)		noncoding transcript	Het
Gsr	T	G	8: 34,170,288 (GRCm39)		probably null	Het
Habp4	G	T	13: 64,332,420 (GRCm39)	V344F	probably benign	Het
Hdac7	G	A	15: 97,704,386 (GRCm39)	Q495*	probably null	Het
Helb	T	C	10: 119,930,168 (GRCm39)	D737G	possibly damaging	Het
Hltf	A	G	3: 20,160,610 (GRCm39)	D759G	probably damaging	Het
Hlx	G	T	1: 184,464,184 (GRCm39)	A52D	probably damaging	Het
Itga10	C	T	3: 96,559,054 (GRCm39)		probably benign	Het
Itsn2	A	G	12: 4,722,733 (GRCm39)		probably benign	Het
Kank2	A	T	9: 21,705,857 (GRCm39)	V387E	probably damaging	Het
Lefty1	T	C	1: 180,765,389 (GRCm39)	V319A	probably benign	Het
Lonp1	T	C	17: 56,922,068 (GRCm39)	T771A	possibly damaging	Het
Lpcat2b	A	T	5: 107,581,716 (GRCm39)	K348N	possibly damaging	Het
Lsamp	T	C	16: 41,709,430 (GRCm39)	V103A	probably damaging	Het
Ltbp4	A	T	7: 27,026,195 (GRCm39)	C538S	probably damaging	Het
Micu1	T	C	10: 59,604,035 (GRCm39)	S174P	probably damaging	Het
Mta1	A	G	12: 113,099,926 (GRCm39)	N607S	probably damaging	Het
Muc5b	C	T	7: 141,416,891 (GRCm39)	S3279L	probably benign	Het
Naalad2	T	C	9: 18,289,995 (GRCm39)	E211G	probably damaging	Het
Nup155	T	A	15: 8,165,311 (GRCm39)	M649K	probably benign	Het
Pan2	T	C	10: 128,156,282 (GRCm39)	V1171A	probably damaging	Het
Pisd	A	G	5: 32,896,209 (GRCm39)	V372A	probably damaging	Het
Rab23	T	A	1: 33,763,019 (GRCm39)	C30S	probably damaging	Het
Sacs	A	G	14: 61,440,344 (GRCm39)	T797A	probably benign	Het
Sall3	T	C	18: 81,015,108 (GRCm39)	D940G	probably benign	Het
Scn1a	T	C	2: 66,161,615 (GRCm39)	E311G	probably benign	Het
Sdk1	T	A	5: 142,129,573 (GRCm39)	I1598N	probably damaging	Het
Slc22a17	A	T	14: 55,145,957 (GRCm39)		probably null	Het
Slc36a4	T	A	9: 15,645,506 (GRCm39)	V311D	probably damaging	Het
Sprr3	T	A	3: 92,364,253 (GRCm39)	Q197L	possibly damaging	Het
Stab2	A	C	10: 86,732,360 (GRCm39)		probably null	Het
Stk4	C	T	2: 163,942,448 (GRCm39)	T360M	probably benign	Het
Tas2r123	T	A	6: 132,824,295 (GRCm39)	V64D	probably damaging	Het
Trhde	T	G	10: 114,424,336 (GRCm39)	N483T	possibly damaging	Het
Trp53	C	T	11: 69,479,323 (GRCm39)	T167M	probably damaging	Het
Tspan8	A	G	10: 115,680,035 (GRCm39)	I217V	probably benign	Het
Tut4	T	C	4: 108,336,720 (GRCm39)	L148P	probably benign	Het
Usp17la	A	G	7: 104,509,527 (GRCm39)	E44G	possibly damaging	Het
Usp40	T	G	1: 87,906,258 (GRCm39)	Q659P	probably benign	Het
Vmn1r4	T	C	6: 56,933,723 (GRCm39)	C76R	probably damaging	Het
Vmn2r118	C	T	17: 55,899,925 (GRCm39)	G660R	probably damaging	Het
Zfp786	T	A	6: 47,796,691 (GRCm39)	H749L	probably 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
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
R7179:Prim1	UTSW	10	127,851,845 (GRCm39)	missense	probably damaging	1.00
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'- GTTCCACAGTTCACCTCAGC -3'
(R):5'- AGCCAACAGGTCGACTCTTC -3'

Sequencing Primer
(F):5'- ACAGTTCACCTCAGCGCTGG -3'
(R):5'- TTGCTAACACATACTGATCCAGTCGG -3'

Posted On

2014-08-25