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Optic atrophy (PheCode 377.1)

near LINC02063 · rs144654840

Stands on its own. Nothing else here links to this position yet — but the page above is the point: what the research found, what each genotype means, and where it came from, in language you can read. Links to conditions, drugs and the senses appear automatically if we write them.

Strength of the evidence

1 / 4

Its strongest genetic-study result is p = 10−11, with 1 associations in the GWAS Catalog.

How this is scored

4: ClinVar disease-causing, reviewed by an expert panel or a guideline (3–4 stars). 3: ClinVar, several labs agreeing (2 stars), or a genetic study at p ≤ 10−50. 2: ClinVar from one lab (1 star), or p ≤ 10−20. 1: ClinVar submitted without criteria (0 stars), or genome-wide significance (p ≤ 5×10−8). The higher of the two counts. It says how solid the evidence is, not whether it matters for a particular person.

What the study found

Who was studied 2,374 African American or Afro-Caribbean cases, 117,039 African American or Afro-Caribbean controls, 4,922 European ancestry cases, 440,844 European ancestry controls, 535 Hispanic or Latin American cases, 58,733 Hispanic or Latin American controls.

The effect Each copy of the T allele shifted the measure 1.75 lower (95% confidence interval 1.69-1.82); p = 3 × 10−11.

How common The T allele had a frequency of about 100% in the people studied.

Where it sits Chromosome 5, band 5p15.33 — between genes, 197 kb from LINC02063.

How common each version is

AT
World gnomAD
A 0.0% · T 100.0%
World 1000 Genomes
A 0.0% · T 100.0%
World TOPMed
A 0.0% · T 100.0%

The share of all copies of this position that are each version. Source: the population studies published in dbSNP (US NCBI); each row names its study. No Korean figure for this position yet.

What each result means

A/A No copy of the version the research linked to Optic atrophy (PheCode 377.1). This is the starting point the study compared everyone against.
A/T One copy of the version the research linked to Optic atrophy (PheCode 377.1). That is a smaller link than two copies.
T/T Two copies of the version the research linked to Optic atrophy (PheCode 377.1). That is the strongest link of the three results. A link in a study is not a diagnosis.
Source
Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program
Verma A, Huffman JE, Rodriguez A, Conery M, Liu M, Ho YL, Kim Y, Heise DA, Guare L, Panickan VA, Garcon H, Linares F
and 59 more — show all
Costa L, Goethert I, Tipton R, Honerlaw J, Davies L, Whitbourne S, Cohen J, Posner DC, Sangar R, Murray M, Wang X, Dochtermann DR, Devineni P, Shi Y, Nandi TN, Assimes TL, Brunette CA, Carroll RJ, Clifford R, Duvall S, Gelernter J, Hung A, Iyengar SK, Joseph J, Kember R, Kranzler H, Kripke CM, Levey D, Luoh SW, Merritt VC, Overstreet C, Deak JD, Grant SFA, Polimanti R, Roussos P, Shakt G, Sun YV, Tsao N, Venkatesh S, Voloudakis G, Justice A, Begoli E, Ramoni R, Tourassi G, Pyarajan S, Tsao P, O'Donnell CJ, Muralidhar S, Moser J, Casas JP, Bick AG, Zhou W, Cai T, Voight BF, Cho K, Gaziano JM, Madduri RK, Damrauer S, Liao KP
Science (New York, N.Y.) · 2024 · PMID 39024449 · open access

Quoting this page

Licensed CC BY-NC 4.0: free to read, share and adapt for non-commercial use, naming MyGeneLog™ and linking the exact page. Commercial use, including training or serving a commercial AI system, needs a licence — https://www.mygenelog.com/license

Optic atrophy (PheCode 377.1) (rs144654840). MyGeneLog™. https://www.mygenelog.com/variants/rs144654840

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