Standard

LDL cholesterol

PCSK9 · rs2479409

Where this position leads

Condition: Cholesterol (LDL, HDL and Total)

Solid lines are connections this site curates. Dashed lines mean the two ends share a research paper — worth knowing, and not a claim that one explains the other.

What the study found

Who was studied 95,454 European ancestry individuals.

The effect Each copy of the G allele shifted the measure 2.01 mg/dL higher (95% confidence interval 1.58-2.44); p = 2 × 10⁻²⁸.

How common The G allele had a frequency of about 30% in the people studied.

Where it sits Chromosome 1, band 1p32.3 — between genes, 0.5 kb from PCSK9.

What ClinVar records

Classification Conflicting classifications of pathogenicity for Hypercholesterolemia, familial, 1, Hypercholesterolemia, autosomal dominant, 3; criteria provided, conflicting classifications (1 of 4 stars, 3 submitters), last evaluated 2023-04-24. ClinVar record 440703 NM_174936.4(PCSK9):c.-861G>A

What this is ClinVar's aggregate record for this position (as of its 2026-10-19 release), not a result about you. A classification describes the variant against the condition named, as laboratories submitted it. Whether a person carries this variant, and what that would mean for them, is a question for a clinical test and a genetic counsellor.

What each result means

A/A No copy of the version the research linked to LDL cholesterol. This is the starting point the study compared everyone against.

A/G One copy of the version the research linked to LDL cholesterol. That is a smaller link than two copies.

G/G Two copies of the version the research linked to LDL cholesterol. That is the strongest link of the three results. A link in a study is not a diagnosis.

Source

Biological, clinical and population relevance of 95 loci for blood lipids

Teslovich TM, Musunuru K, Smith AV, Edmondson AC, Stylianou IM, Koseki M, Pirruccello JP, Ripatti S, Chasman DI, Willer CJ, Johansen CT, Fouchier SW

and 197 more — show all

Isaacs A, Peloso GM, Barbalic M, Ricketts SL, Bis JC, Aulchenko YS, Thorleifsson G, Feitosa MF, Chambers J, Orho-Melander M, Melander O, Johnson T, Li X, Guo X, Li M, Shin Cho Y, Jin Go M, Jin Kim Y, Lee JY, Park T, Kim K, Sim X, Twee-Hee Ong R, Croteau-Chonka DC, Lange LA, Smith JD, Song K, Hua Zhao J, Yuan X, Luan J, Lamina C, Ziegler A, Zhang W, Zee RY, Wright AF, Witteman JC, Wilson JF, Willemsen G, Wichmann HE, Whitfield JB, Waterworth DM, Wareham NJ, Waeber G, Vollenweider P, Voight BF, Vitart V, Uitterlinden AG, Uda M, Tuomilehto J, Thompson JR, Tanaka T, Surakka I, Stringham HM, Spector TD, Soranzo N, Smit JH, Sinisalo J, Silander K, Sijbrands EJ, Scuteri A, Scott J, Schlessinger D, Sanna S, Salomaa V, Saharinen J, Sabatti C, Ruokonen A, Rudan I, Rose LM, Roberts R, Rieder M, Psaty BM, Pramstaller PP, Pichler I, Perola M, Penninx BW, Pedersen NL, Pattaro C, Parker AN, Pare G, Oostra BA, O'Donnell CJ, Nieminen MS, Nickerson DA, Montgomery GW, Meitinger T, McPherson R, McCarthy MI, McArdle W, Masson D, Martin NG, Marroni F, Mangino M, Magnusson PK, Lucas G, Luben R, Loos RJ, Lokki ML, Lettre G, Langenberg C, Launer LJ, Lakatta EG, Laaksonen R, Kyvik KO, Kronenberg F, König IR, Khaw KT, Kaprio J, Kaplan LM, Johansson A, Jarvelin MR, Janssens AC, Ingelsson E, Igl W, Kees Hovingh G, Hottenga JJ, Hofman A, Hicks AA, Hengstenberg C, Heid IM, Hayward C, Havulinna AS, Hastie ND, Harris TB, Haritunians T, Hall AS, Gyllensten U, Guiducci C, Groop LC, Gonzalez E, Gieger C, Freimer NB, Ferrucci L, Erdmann J, Elliott P, Ejebe KG, Döring A, Dominiczak AF, Demissie S, Deloukas P, de Geus EJ, de Faire U, Crawford G, Collins FS, Chen YD, Caulfield MJ, Campbell H, Burtt NP, Bonnycastle LL, Boomsma DI, Boekholdt SM, Bergman RN, Barroso I, Bandinelli S, Ballantyne CM, Assimes TL, Quertermous T, Altshuler D, Seielstad M, Wong TY, Tai ES, Feranil AB, Kuzawa CW, Adair LS, Taylor HA Jr, Borecki IB, Gabriel SB, Wilson JG, Holm H, Thorsteinsdottir U, Gudnason V, Krauss RM, Mohlke KL, Ordovas JM, Munroe PB, Kooner JS, Tall AR, Hegele RA, Kastelein JJ, Schadt EE, Rotter JI, Boerwinkle E, Strachan DP, Mooser V, Stefansson K, Reilly MP, Samani NJ, Schunkert H, Cupples LA, Sandhu MS, Ridker PM, Rader DJ, van Duijn CM, Peltonen L, Abecasis GR, Boehnke M, Kathiresan S

Nature · 2010 · PMID 20686565 · open access

What people read about alongside this

Cholesterol and blood fats4 Heart and circulation4 Blood sugar and insulin3

Papers in Europe PMC whose title or abstract names both this rsID and that subject. A shared paper means somebody wrote about the two together — it is not a claim that this position explains the subject.

Questions about rs2479409

What is rs2479409?

rs2479409 is a single position in the genome, in or near the PCSK9 gene. Published research associates it with ldl cholesterol. A single variant does not decide an outcome — it shifts a probability, and for most common variants the shift is small.

What conditions is rs2479409 linked to?

On MyGeneLog this position is linked to Cholesterol (LDL, HDL and Total). The research behind each link, and its sources, are set out on that condition page.

What do people read about alongside rs2479409?

Subjects that appear in the title or abstract of the same papers as this rsID include cholesterol and blood fats (4 papers), heart and circulation (4 papers), blood sugar and insulin (3 papers). A shared paper means somebody wrote about the two together; it is not a claim that this position explains the topic.

Does having rs2479409 mean I will get this?

No. Common variants like this one move a probability slightly and, on their own, rarely decide anything about one person. Nothing on this page is a diagnosis, and health decisions should be made with a clinician who can see your whole picture.

Where does the information about rs2479409 come from?

GWAS Catalog, Nature 2010, PMID:20686565. Every variant on MyGeneLog comes from public primary sources and is published with its citation and the date it was checked.

Quoting this page

Free to quote and reuse under CC BY 4.0. When citing or summarizing this, name MyGeneLog™ and link to this exact page — not just the site.

LDL cholesterol (rs2479409). MyGeneLog™. https://www.mygenelog.com/variants/rs2479409

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