Mutagenetix > Incidental Mutation

Incidental Mutation 'D3080:Pcm1'

125

Institutional Source

Beutler Lab

Gene Symbol

Pcm1

Ensembl Gene

ENSMUSG00000031592

Gene Name

pericentriolar material 1

Synonyms

9430077F19Rik, C030044G17Rik, 2600002H09Rik

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

D3080 of strain grasshopper

Quality Score

Status

Validated

Chromosome

Chromosomal Location

41692789-41785381 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 41728976 bp (GRCm39)

Zygosity

Homozygous

Amino Acid Change

Asparagine to Lysine at position 649 (N649K)

Ref Sequence

ENSEMBL: ENSMUSP00000147887 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000045218] [ENSMUST00000211247]

AlphaFold

Q9R0L6

Predicted Effect

probably damaging
Transcript: ENSMUST00000045218
AA Change: N610K

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

SMART Domains

Protein: ENSMUSP00000039709
Gene: ENSMUSG00000031592
AA Change: N610K

Domain	Start	End	E-Value	Type
coiled coil region	218	238	N/A	INTRINSIC
coiled coil region	270	301	N/A	INTRINSIC
coiled coil region	399	426	N/A	INTRINSIC
coiled coil region	492	520	N/A	INTRINSIC
low complexity region	527	548	N/A	INTRINSIC
low complexity region	622	647	N/A	INTRINSIC
coiled coil region	652	683	N/A	INTRINSIC
coiled coil region	724	772	N/A	INTRINSIC
coiled coil region	822	856	N/A	INTRINSIC
coiled coil region	988	1017	N/A	INTRINSIC
low complexity region	1021	1033	N/A	INTRINSIC
low complexity region	1287	1301	N/A	INTRINSIC
Pfam:PCM1_C	1369	1999	3.6e-295	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000211090

Predicted Effect

probably damaging
Transcript: ENSMUST00000211247
AA Change: N649K

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

Meta Mutation Damage Score

0.1246

Coding Region Coverage

1x: 88.9%
3x: 76.7%

Validation Efficiency

82% (141/173)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a component of centriolar satellites, which are electron dense granules scattered around centrosomes. Inhibition studies show that this protein is essential for the correct localization of several centrosomal proteins, and for anchoring microtubules to the centrosome. Chromosomal aberrations involving this gene are associated with papillary thyroid carcinomas and a variety of hematological malignancies, including atypical chronic myeloid leukemia and T-cell lymphoma. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

Allele List at MGI

All alleles(34) : Gene trapped(34)

Other mutations in this stock

Total: 20 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310003L06Rik	C	A	5: 88,119,846 (GRCm39)	P201Q	possibly damaging	Het
Bdp1	A	T	13: 100,160,129 (GRCm39)	S2417R	probably benign	Het
Ccdc168	C	A	1: 44,106,495 (GRCm39)			Het
Dscaml1	A	T	9: 45,595,623 (GRCm39)	H783L	probably benign	Het
Fbxl5	A	T	5: 43,915,708 (GRCm39)	M568K	probably benign	Het
Gab1	T	A	8: 81,493,007 (GRCm39)	D710V	probably damaging	Homo
Gabrr2	T	C	4: 33,084,466 (GRCm39)	F128S	probably damaging	Het
Hyou1	T	A	9: 44,295,774 (GRCm39)	V343E	probably damaging	Het
Nlrp4a	A	G	7: 26,143,766 (GRCm39)	T44A	probably benign	Het
Nsd3	C	A	8: 26,203,572 (GRCm39)	T1362N	possibly damaging	Homo
Or6f2	G	A	7: 139,756,275 (GRCm39)	V81M	possibly damaging	Het
Pde4dip	T	C	3: 97,674,146 (GRCm39)	K257E	probably damaging	Het
Pfpl	G	A	19: 12,406,196 (GRCm39)	R149Q	probably damaging	Homo
Pou2f2	G	T	7: 24,796,558 (GRCm39)		probably benign	Het
Rptn	A	G	3: 93,303,135 (GRCm39)	D156G	possibly damaging	Het
Sec31a	T	C	5: 100,511,691 (GRCm39)	D1107G	probably damaging	Het
Smyd3	A	G	1: 178,913,987 (GRCm39)	Y239H	probably damaging	Het
Stoml3	T	C	3: 53,405,415 (GRCm39)	F32S	probably benign	Het
Tnnc1	C	A	14: 30,932,147 (GRCm39)	D62E	probably damaging	Homo
Vsig10	C	T	5: 117,481,884 (GRCm39)	A358V	probably damaging	Het

Other mutations in Pcm1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00773:Pcm1	APN	8	41,727,314 (GRCm39)	missense	probably damaging	1.00
IGL00852:Pcm1	APN	8	41,740,858 (GRCm39)	missense	probably damaging	1.00
IGL00896:Pcm1	APN	8	41,729,160 (GRCm39)	missense	possibly damaging	0.70
IGL00927:Pcm1	APN	8	41,740,918 (GRCm39)	missense	probably damaging	1.00
IGL01085:Pcm1	APN	8	41,762,640 (GRCm39)	missense	probably damaging	1.00
IGL01684:Pcm1	APN	8	41,710,960 (GRCm39)	missense	probably benign	0.00
IGL01888:Pcm1	APN	8	41,710,993 (GRCm39)	missense	probably damaging	0.98
IGL02349:Pcm1	APN	8	41,741,192 (GRCm39)	critical splice donor site	probably null
IGL02562:Pcm1	APN	8	41,778,405 (GRCm39)	missense	probably damaging	1.00
IGL02807:Pcm1	APN	8	41,783,919 (GRCm39)	missense	probably damaging	1.00
IGL03081:Pcm1	APN	8	41,728,097 (GRCm39)	missense	probably damaging	1.00
R0090_Pcm1_148	UTSW	8	41,709,078 (GRCm39)	missense	probably damaging	0.99
R1534_pcm1_826	UTSW	8	41,740,738 (GRCm39)	missense	probably benign
R8169_pcm1_970	UTSW	8	41,763,153 (GRCm39)	missense	possibly damaging	0.58
shaved	UTSW	8	41,741,193 (GRCm39)	critical splice donor site	probably null
P0045:Pcm1	UTSW	8	41,741,134 (GRCm39)	missense	probably damaging	0.99
R0090:Pcm1	UTSW	8	41,709,078 (GRCm39)	missense	probably damaging	0.99
R0109:Pcm1	UTSW	8	41,710,974 (GRCm39)	missense	possibly damaging	0.88
R0373:Pcm1	UTSW	8	41,729,148 (GRCm39)	nonsense	probably null
R0386:Pcm1	UTSW	8	41,769,060 (GRCm39)	missense	probably damaging	1.00
R0452:Pcm1	UTSW	8	41,778,942 (GRCm39)	missense	probably benign	0.25
R0498:Pcm1	UTSW	8	41,746,806 (GRCm39)	missense	probably benign	0.01
R0528:Pcm1	UTSW	8	41,768,967 (GRCm39)	missense	probably damaging	1.00
R0587:Pcm1	UTSW	8	41,739,088 (GRCm39)	missense	probably damaging	0.99
R0635:Pcm1	UTSW	8	41,720,216 (GRCm39)	splice site	probably benign
R0725:Pcm1	UTSW	8	41,740,848 (GRCm39)	missense	probably damaging	1.00
R0762:Pcm1	UTSW	8	41,714,057 (GRCm39)	missense	probably damaging	1.00
R0848:Pcm1	UTSW	8	41,735,720 (GRCm39)	missense	probably damaging	1.00
R1027:Pcm1	UTSW	8	41,746,482 (GRCm39)	splice site	probably benign
R1056:Pcm1	UTSW	8	41,774,937 (GRCm39)	missense	probably damaging	1.00
R1534:Pcm1	UTSW	8	41,740,738 (GRCm39)	missense	probably benign
R1566:Pcm1	UTSW	8	41,743,810 (GRCm39)	missense	probably damaging	1.00
R1595:Pcm1	UTSW	8	41,762,672 (GRCm39)	missense	probably damaging	1.00
R1719:Pcm1	UTSW	8	41,766,396 (GRCm39)	missense	possibly damaging	0.62
R1816:Pcm1	UTSW	8	41,762,574 (GRCm39)	missense	probably damaging	0.99
R2177:Pcm1	UTSW	8	41,729,002 (GRCm39)	missense	probably benign
R2495:Pcm1	UTSW	8	41,746,616 (GRCm39)	missense	probably benign
R3737:Pcm1	UTSW	8	41,714,080 (GRCm39)	nonsense	probably null
R3747:Pcm1	UTSW	8	41,785,041 (GRCm39)	missense	probably benign	0.44
R3763:Pcm1	UTSW	8	41,733,114 (GRCm39)	missense	probably damaging	1.00
R3764:Pcm1	UTSW	8	41,783,919 (GRCm39)	missense	probably damaging	1.00
R3798:Pcm1	UTSW	8	41,711,051 (GRCm39)	missense	possibly damaging	0.66
R3968:Pcm1	UTSW	8	41,778,867 (GRCm39)	missense	probably damaging	1.00
R4760:Pcm1	UTSW	8	41,740,775 (GRCm39)	missense	probably damaging	0.99
R4798:Pcm1	UTSW	8	41,746,715 (GRCm39)	missense	probably damaging	1.00
R5062:Pcm1	UTSW	8	41,712,297 (GRCm39)	missense	probably damaging	0.99
R5221:Pcm1	UTSW	8	41,741,193 (GRCm39)	critical splice donor site	probably null
R5250:Pcm1	UTSW	8	41,765,242 (GRCm39)	missense	probably damaging	0.99
R5466:Pcm1	UTSW	8	41,725,499 (GRCm39)	critical splice donor site	probably null
R5470:Pcm1	UTSW	8	41,740,720 (GRCm39)	missense	probably damaging	1.00
R5958:Pcm1	UTSW	8	41,782,016 (GRCm39)	missense	probably damaging	1.00
R6043:Pcm1	UTSW	8	41,781,815 (GRCm39)	missense	possibly damaging	0.54
R6179:Pcm1	UTSW	8	41,736,669 (GRCm39)	missense	probably damaging	0.99
R6186:Pcm1	UTSW	8	41,746,830 (GRCm39)	missense	probably benign	0.23
R6227:Pcm1	UTSW	8	41,783,862 (GRCm39)	missense	probably damaging	0.99
R6368:Pcm1	UTSW	8	41,746,581 (GRCm39)	missense	probably benign	0.09
R6438:Pcm1	UTSW	8	41,778,418 (GRCm39)	missense	possibly damaging	0.94
R6459:Pcm1	UTSW	8	41,714,073 (GRCm39)	missense	probably damaging	1.00
R7399:Pcm1	UTSW	8	41,746,547 (GRCm39)	missense	probably benign	0.11
R7401:Pcm1	UTSW	8	41,762,568 (GRCm39)	missense	probably damaging	1.00
R7478:Pcm1	UTSW	8	41,714,410 (GRCm39)	missense	probably benign	0.17
R7570:Pcm1	UTSW	8	41,720,381 (GRCm39)	missense	possibly damaging	0.64
R7648:Pcm1	UTSW	8	41,728,736 (GRCm39)	missense	probably damaging	0.99
R7773:Pcm1	UTSW	8	41,762,610 (GRCm39)	nonsense	probably null
R7779:Pcm1	UTSW	8	41,782,061 (GRCm39)	missense	probably damaging	1.00
R7842:Pcm1	UTSW	8	41,780,621 (GRCm39)	missense	possibly damaging	0.54
R7863:Pcm1	UTSW	8	41,714,163 (GRCm39)	missense	probably damaging	0.99
R8169:Pcm1	UTSW	8	41,763,153 (GRCm39)	missense	possibly damaging	0.58
R8210:Pcm1	UTSW	8	41,766,974 (GRCm39)	missense	probably damaging	1.00
R8303:Pcm1	UTSW	8	41,736,758 (GRCm39)	missense	probably damaging	1.00
R8397:Pcm1	UTSW	8	41,736,616 (GRCm39)	missense	probably damaging	1.00
R8489:Pcm1	UTSW	8	41,766,437 (GRCm39)	missense	probably benign	0.19
R8519:Pcm1	UTSW	8	41,728,976 (GRCm39)	missense	probably damaging	1.00
R9136:Pcm1	UTSW	8	41,732,825 (GRCm39)	missense	probably benign	0.19
R9245:Pcm1	UTSW	8	41,732,877 (GRCm39)	missense	probably damaging	0.99
R9263:Pcm1	UTSW	8	41,732,790 (GRCm39)	missense	probably benign	0.00
R9406:Pcm1	UTSW	8	41,728,722 (GRCm39)	missense	probably damaging	0.99
R9412:Pcm1	UTSW	8	41,740,788 (GRCm39)	missense	probably damaging	1.00
R9541:Pcm1	UTSW	8	41,780,616 (GRCm39)	missense	probably benign	0.09
R9698:Pcm1	UTSW	8	41,723,541 (GRCm39)	missense	possibly damaging	0.95
R9716:Pcm1	UTSW	8	41,728,168 (GRCm39)	missense	probably damaging	0.98
R9747:Pcm1	UTSW	8	41,757,135 (GRCm39)	missense	probably benign	0.00
R9781:Pcm1	UTSW	8	41,720,398 (GRCm39)	missense	probably damaging	0.99
X0025:Pcm1	UTSW	8	41,783,679 (GRCm39)	missense	probably damaging	1.00
Z1177:Pcm1	UTSW	8	41,740,781 (GRCm39)	missense	probably damaging	0.99
Z1177:Pcm1	UTSW	8	41,727,208 (GRCm39)	missense	possibly damaging	0.94

Nature of Mutation

DNA sequencing using the SOLiD technique identified a G to T transversion at position 2055 of the Pcm1 transcript in exon 12 of 38 total exons. Two transcripts of the Pcm1 gene are displayed on Ensembl. The mutated nucleotide causes an asparagine to lysine substitution at amino acid 610 of the encoded protein. The mutation has been confirmed by DNA sequencing using the Sanger method (Figure 1).

Protein Function and Prediction

The Pcm1 gene encodes a 2025 amino acid protein that belongs to the PCM1 family. PCM1 is required for centrosome assembly and function. It is required for the correct localization of several centrosomal proteins and to anchor microtubules to the centrosome (Uniprot Q9R0L6).

The N610K change is predicted to be probably damaging by the PolyPhen program.

Posted On

2010-03-12