UniProtKB/Swiss-Prot P09603: Variant p.Phe489Ser

Macrophage colony-stimulating factor 1
Gene: CSF1
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Variant information Variant position:

489 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant:

LB/B The variants are classified into three categories: LP/P, LB/B and US.

LP/P: likely pathogenic or pathogenic.
LB/B: likely benign or benign.
US: uncertain significance

Residue change:

From Phenylalanine (F) to Serine (S) at position 489 (F489S, p.Phe489Ser). Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss-Prot are those adopted by the commission on Biochemical Nomenclature of the IUPAC-IUB.
Physico-chemical properties:

Change from large size and aromatic (F) to small size and polar (S) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score:

-2 The score within a Blosum matrix for the corresponding wild-type to variant amino acid change. The log-odds score measures the logarithm for the ratio of the likelihood of two amino acids appearing by chance. The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid with another:

Lowest score: -4 (low probability of substitution).
Highest score: 11 (high probability of substitution).

More information can be found on the following page
Other resources:

Links to websites of interest for the variant.

Variant rs333971 [ dbSNP | Ensembl ]

Sequence information Variant position:

489 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length:

554 The length of the canonical sequence.
Location on the sequence:

PRFNSVPLTDTGHERQSEGS F SPQLQESVFHLLVPSVILVL The residue change on the sequence. Unless the variant is located at the beginning or at the end of the protein sequence, both residues upstream (20) and downstream (20) of the variant will be shown.
Residue conservation:

The multiple alignment of the region surrounding the variant against various orthologous sequences.

Human                         PRFN----------------------------------SVPLTDTGHERQSEGSFSPQLQESVFHL--LVPSVIL---------------------------------VL

Mouse                         ARFN----------------------------------SIP

Rat                           ARFN----------------------------------SIP

Baker's yeast                 SLFDVEVLVIRIDKVSIRSETHSGKKLKTDLQLQVLDVSAA

Sequence annotation in neighborhood:

The regions or sites of interest surrounding the variant. In general the features listed are posttranslational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. The "Sequence annotation in neighborhood" lines have a fixed format:

Type: the type of sequence feature.
Positions: endpoints of the sequence feature.
Description: contains additional information about the feature.

Type	Positions	Description
Chain	33 – 554	Macrophage colony-stimulating factor 1
Topological domain	33 – 496	Lumenal
Mutagenesis	489 – 554	Missing. Produces biologically active protein which is secreted.

Literature citations
Molecular cloning of a complementary DNA encoding human macrophage-specific colony-stimulating factor (CSF-1).
Kawasaki E.S.; Ladner M.B.; Wang A.M.; van Arsdell J.N.; Warren M.K.; Coyne M.Y.; Schweickart V.L.; Lee M.-T.; Wilson K.J.; Boosman A.; Stanley E.R.; Ralph P.; Mark D.F.;
Science 230:291-296(1985)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; PROTEIN SEQUENCE OF 33-44 (ISOFORM 3); VARIANT SER-489; Human CSF-1: molecular cloning and expression of 4-kb cDNA encoding the human urinary protein.
Wong G.G.; Temple P.A.; Leary A.C.; Witek-Giannotti J.S.; Yang Y.C.; Ciarletta A.B.; Chung M.; Murtha P.; Kriz R.; Kaufman R.J.; Ferenz C.R.; Sibley B.S.; Turner K.J.; Hewick R.M.; Clark S.C.; Yanai N.; Yokota H.; Yamada M.; Saito M.; Motoyoshi K.; Takaku F.;
Science 235:1504-1508(1987)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); PARTIAL PROTEIN SEQUENCE; VARIANT SER-489; Human macrophage-colony stimulating factor: alternative RNA and protein processing from a single gene.
Cerretti D.P.; Wignall J.; Anderson D.; Tushinski R.J.; Gallis B.M.; Stya M.; Gillis S.; Urdal D.L.; Cosman D.;
Mol. Immunol. 25:761-770(1988)
Cited for: NUCLEOTIDE SEQUENCE [MRNA]; ALTERNATIVE SPLICING; MUTAGENESIS OF ISOFORM 3; VARIANT SER-489; Amino-terminal region of human macrophage colony-stimulating factor (M-CSF) is sufficient for its in vitro biological activity: molecular cloning and expression of carboxyl-terminal deletion mutants of human M-CSF.
Takahashi M.; Hirato T.; Takano M.; Nishida T.; Nagamura K.; Kamogashira T.; Nakai S.; Hirai Y.;
Biochem. Biophys. Res. Commun. 161:892-901(1989)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); VARIANTS PRO-408 AND SER-489; Complete sequencing and characterization of 21,243 full-length human cDNAs.
Ota T.; Suzuki Y.; Nishikawa T.; Otsuki T.; Sugiyama T.; Irie R.; Wakamatsu A.; Hayashi K.; Sato H.; Nagai K.; Kimura K.; Makita H.; Sekine M.; Obayashi M.; Nishi T.; Shibahara T.; Tanaka T.; Ishii S.; Yamamoto J.; Saito K.; Kawai Y.; Isono Y.; Nakamura Y.; Nagahari K.; Murakami K.; Yasuda T.; Iwayanagi T.; Wagatsuma M.; Shiratori A.; Sudo H.; Hosoiri T.; Kaku Y.; Kodaira H.; Kondo H.; Sugawara M.; Takahashi M.; Kanda K.; Yokoi T.; Furuya T.; Kikkawa E.; Omura Y.; Abe K.; Kamihara K.; Katsuta N.; Sato K.; Tanikawa M.; Yamazaki M.; Ninomiya K.; Ishibashi T.; Yamashita H.; Murakawa K.; Fujimori K.; Tanai H.; Kimata M.; Watanabe M.; Hiraoka S.; Chiba Y.; Ishida S.; Ono Y.; Takiguchi S.; Watanabe S.; Yosida M.; Hotuta T.; Kusano J.; Kanehori K.; Takahashi-Fujii A.; Hara H.; Tanase T.-O.; Nomura Y.; Togiya S.; Komai F.; Hara R.; Takeuchi K.; Arita M.; Imose N.; Musashino K.; Yuuki H.; Oshima A.; Sasaki N.; Aotsuka S.; Yoshikawa Y.; Matsunawa H.; Ichihara T.; Shiohata N.; Sano S.; Moriya S.; Momiyama H.; Satoh N.; Takami S.; Terashima Y.; Suzuki O.; Nakagawa S.; Senoh A.; Mizoguchi H.; Goto Y.; Shimizu F.; Wakebe H.; Hishigaki H.; Watanabe T.; Sugiyama A.; Takemoto M.; Kawakami B.; Yamazaki M.; Watanabe K.; Kumagai A.; Itakura S.; Fukuzumi Y.; Fujimori Y.; Komiyama M.; Tashiro H.; Tanigami A.; Fujiwara T.; Ono T.; Yamada K.; Fujii Y.; Ozaki K.; Hirao M.; Ohmori Y.; Kawabata A.; Hikiji T.; Kobatake N.; Inagaki H.; Ikema Y.; Okamoto S.; Okitani R.; Kawakami T.; Noguchi S.; Itoh T.; Shigeta K.; Senba T.; Matsumura K.; Nakajima Y.; Mizuno T.; Morinaga M.; Sasaki M.; Togashi T.; Oyama M.; Hata H.; Watanabe M.; Komatsu T.; Mizushima-Sugano J.; Satoh T.; Shirai Y.; Takahashi Y.; Nakagawa K.; Okumura K.; Nagase T.; Nomura N.; Kikuchi H.; Masuho Y.; Yamashita R.; Nakai K.; Yada T.; Nakamura Y.; Ohara O.; Isogai T.; Sugano S.;
Nat. Genet. 36:40-45(2004)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1); VARIANT SER-489; Submission
Mural R.J.; Istrail S.; Sutton G.G.; Florea L.; Halpern A.L.; Mobarry C.M.; Lippert R.; Walenz B.; Shatkay H.; Dew I.; Miller J.R.; Flanigan M.J.; Edwards N.J.; Bolanos R.; Fasulo D.; Halldorsson B.V.; Hannenhalli S.; Turner R.; Yooseph S.; Lu F.; Nusskern D.R.; Shue B.C.; Zheng X.H.; Zhong F.; Delcher A.L.; Huson D.H.; Kravitz S.A.; Mouchard L.; Reinert K.; Remington K.A.; Clark A.G.; Waterman M.S.; Eichler E.E.; Adams M.D.; Hunkapiller M.W.; Myers E.W.; Venter J.C.;
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]; VARIANT SER-489; The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
The MGC Project Team;
Genome Res. 14:2121-2127(2004)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1); VARIANT SER-489; Human CSF-1: gene structure and alternative splicing of mRNA precursors.
Ladner M.B.; Martin G.A.; Noble J.A.; Nikoloff D.M.; Tal R.; Kawasaki E.S.; White T.J.;
EMBO J. 6:2693-2698(1987)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] OF 1-13 AND 19-554 (ISOFORM 1); VARIANT SER-489; Expression of colony-stimulating factor-1 (CSF-1) messenger RNA in human endometrial glands during the menstrual cycle: molecular cloning of a novel transcript that predicts a cell surface form of CSF-1.
Pampfer S.; Tabibzadeh S.; Chuan F.-C.; Pollard J.W.;
Mol. Endocrinol. 5:1931-1938(1991)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 13-554 (ISOFORM 3); VARIANT SER-489;

Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.